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26 files changed, 84996 insertions, 1 deletions
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+table tr:hover.covered .num{ + background-color:rgba(95,151,68,0.7) +} +table tr.missed td{ + background-color:rgba(185,73,71,0.3) +} +table tr:hover.missed .num{ + background-color:rgba(185,73,71,0.7) +} + +table tr.missed:hover td{ + -webkit-box-shadow:0 -2px 0 0 #b94947 inset; + -moz-box-shadow:0 -2px 0 0 #b94947 inset; + box-shadow:0 -2px 0 0 #b94947 inset +} +table tr.covered:hover td{ + -webkit-box-shadow:0 -2px 0 0 #5f9744 inset; + -moz-box-shadow:0 -2px 0 0 #5f9744 inset; + box-shadow:0 -2px 0 0 #5f9744 inset +} + +table tr.never td{ + background-color:transparent +} + +table tbody { + border-style: solid; + border: 1px solid rgba(0,0,0,0.1) +} + +table .num { + border-right: 1px solid rgba(0,0,0,0.1) +} + +td.coverage em { + opacity: 0.5; +} + +table td.coverage { + border-right: 1px solid rgba(0,0,0,0.1); + font-weight: bold; + text-align: center; +} +table.table-condensed pre { + background-color: transparent; + margin: 0; + padding: 0; + border: 0; + font-size: 11px; +} +div#files td { + padding: 0; + padding-left: 5px; +} + +div#files td.num { + padding-right: 5px; +} + +table.table-condensed { + font-size: 11px; +}</style> + <div class="col-md-8 col-md-offset-2"> + <h2>mkin coverage - 89.32%</h2> + <div class="tabbable"> + <ul class="nav nav-tabs" data-tabsetid="covr"> + <li class="active"> + <a href="#tab-covr-1" data-toggle="tab" data-value="Files">Files</a> + </li> + <li> + <a href="#tab-covr-2" data-toggle="tab" data-value="Source">Source</a> + </li> + </ul> + <div class="tab-content" data-tabsetid="covr"> + <div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1"> + <div class="datatables html-widget html-fill-item" id="htmlwidget-df8b8ed832d104ae69ed" style="width:100%;height:500px;"></div> + <script type="application/json" data-for="htmlwidget-df8b8ed832d104ae69ed">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/summary_listing.R<\/a>","<a 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class=\"row-border\">\n <thead>\n <tr>\n <th>File<\/th>\n <th>Lines<\/th>\n <th>Relevant<\/th>\n <th>Covered<\/th>\n <th>Missed<\/th>\n <th>Hits / Line<\/th>\n <th>Coverage<\/th>\n <\/tr>\n <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n var percent = cellData.replace(\"%\", \"\");\n if (percent > 90) {\n var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n } else if (percent > 75) {\n var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n } else {\n var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n }\n $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]},{"name":"File","targets":0},{"name":"Lines","targets":1},{"name":"Relevant","targets":2},{"name":"Covered","targets":3},{"name":"Missed","targets":4},{"name":"Hits 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</td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Fit nonlinear mixed models with SAEM</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function uses [saemix::saemix()] as a backend for fitting nonlinear mixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' effects models created from [mmkin] row objects using the Stochastic Approximation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Expectation Maximisation algorithm (SAEM).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' An mmkin row object is essentially a list of mkinfit objects that have been</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' obtained by fitting the same model to a list of datasets using [mkinfit].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Starting values for the fixed effects (population mean parameters, argument</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' psi0 of [saemix::saemixModel()] are the mean values of the parameters found</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' using [mmkin].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom utils packageVersion</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom saemix saemix</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An [mmkin] row object containing several fits of the same</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mkinmod] model to different datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose Should we print information about created objects of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' type [saemix::SaemixModel] and [saemix::SaemixData]?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transformations Per default, all parameter transformations are done</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in mkin. If this argument is set to 'saemix', parameter transformations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are done in 'saemix' for the supported cases, i.e. (as of version 1.1.2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO, FOMC, DFOP and HS without fixing `parent_0`, and SFO or DFOP with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' one SFO metabolite.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param error_model Possibility to override the error model used in the mmkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param degparms_start Parameter values given as a named numeric vector will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be used to override the starting values obtained from the 'mmkin' object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param test_log_parms If TRUE, an attempt is made to use more robust starting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' values for population parameters fitted as log parameters in mkin (like</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rate constants) by only considering rate constants that pass the t-test</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' when calculating mean degradation parameters using [mean_degparms].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param conf.level Possibility to adjust the required confidence level</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for parameter that are tested if requested by 'test_log_parms'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param solution_type Possibility to specify the solution type in case the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' automatic choice is not desired</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param no_random_effect Character vector of degradation parameters for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' which there should be no variability over the groups. Only used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if the covariance model is not explicitly specified.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariance.model Will be passed to [saemix::saemixModel()]. Per</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' default, uncorrelated random effects are specified for all degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param omega.init Will be passed to [saemix::saemixModel()]. If using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkin transformations and the default covariance model with optionally</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' excluded random effects, the variances of the degradation parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are estimated using [mean_degparms], with testing of untransformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' log parameters for significant difference from zero. If not using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkin transformations or a custom covariance model, the default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' initialisation of [saemix::saemixModel] is used for omega.init.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariates A data frame with covariate data for use in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'covariate_models', with dataset names as row names.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariate_models A list containing linear model formulas with one explanatory</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variable, i.e. of the type 'parameter ~ covariate'. Covariates must be available</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in the 'covariates' data frame.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param error.init Will be passed to [saemix::saemixModel()].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param quiet Should we suppress the messages saemix prints at the beginning</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and the end of the optimisation process?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param nbiter.saemix Convenience option to increase the number of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' iterations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param control Passed to [saemix::saemix].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further parameters passed to [saemix::saemixModel].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An S3 object of class 'saem.mmkin', containing the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [saemix::SaemixObject] as a list component named 'so'. The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' object also inherits from 'mixed.mmkin'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [summary.saem.mmkin] [plot.mixed.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds <- lapply(experimental_data_for_UBA_2019[6:10],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(x) subset(x$data[c("name", "time", "value")]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(ds) <- paste("Dataset", 6:10)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_sfo <- saem(f_mmkin_parent["SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_sfo, f_saem_fomc, f_saem_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_sfo, f_saem_dfop, test = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_red <- update(f_saem_dfop, no_random_effect = "g_qlogis")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_dfop, f_saem_dfop_red, test = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_sfo, f_saem_fomc, f_saem_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The returned saem.mmkin object contains an SaemixObject, therefore we can use</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # functions from saemix</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(saemix)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_fomc$so, plot.type = "convergence")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_fomc$so, plot.type = "individual.fit")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_fomc$so, plot.type = "npde")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_fomc$so, plot.type = "vpc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_fomc, f_saem_fomc_tc, test = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # and compiled ODEs for FOMC that are much slower</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin <- mmkin(list(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # each on this system, as we use analytical solutions written for saemix.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # When using the analytical solutions written for mkin this took around</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # four minutes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can use print, plot and summary methods to check the results</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_saem_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(f_saem_dfop_sfo, data = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The following takes about 6 minutes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nbiter.saemix = c(200, 80))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #anova(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # f_saem_dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # f_saem_dfop_sfo_deSolve))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # If the model supports it, we can also use eigenvalue based solutions, which</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # take a similar amount of time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r">saem <- function(object, ...) UseMethod("saem")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">saem.mmkin <- function(object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transformations = c("mkin", "saemix"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_start = numeric(),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> test_log_parms = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.level = 0.6,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance.model = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_models = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> no_random_effect = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> error.init = c(1, 1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> nbiter.saemix = c(300, 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> control = list(displayProgress = FALSE, print = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> nbiter.saemix = nbiter.saemix,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> save = FALSE, save.graphs = FALSE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> verbose = FALSE, quiet = FALSE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- match.call()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transformations <- match.arg(transformations)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m_saemix <- saemix_model(object, verbose = verbose,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model = error_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_start = degparms_start,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> test_log_parms = test_log_parms, conf.level = conf.level,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">165</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transformations = transformations,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance.model = covariance.model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init = omega.init,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = covariates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_models = covariate_models,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error.init = error.init,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">2411<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_random_effect = no_random_effect,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_saemix <- saemix_data(object, covariates = covariates, verbose = verbose)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_failed <- FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> FIM_failed <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_time <- system.time({</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> utils::capture.output(f_saemix <- try(saemix(m_saemix, d_saemix, control)), split = !quiet)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">180</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(f_saemix, "try-error")) fit_failed <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_data <- nlme_data(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">185</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!fit_failed) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">186</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(is.na(f_saemix@results@se.fixed))) FIM_failed <- c(FIM_failed, "fixed effects")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(is.na(c(f_saemix@results@se.omega, f_saemix@results@se.respar)))) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">188</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> FIM_failed <- c(FIM_failed, "random effects and error model parameters")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms_optim <- f_saemix@results@fixed.effects</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(transparms_optim) <- f_saemix@results@name.fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms_optim <- backtransform_odeparms(transparms_optim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">774<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms_optim <- transparms_optim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">203</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saemix_data_ds <- f_saemix@data@data$ds</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkin_ds_order <- as.character(unique(return_data$ds))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saemix_ds_order <- unique(saemix_data_ds)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi <- saemix::psi(f_saemix)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(psi) <- saemix_ds_order</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_data$predicted <- f_saemix@model@model(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi = psi[mkin_ds_order, ],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> id = as.numeric(return_data$ds),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xidep = return_data[c("time", "name")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_data <- transform(return_data,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">215</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residual = value - predicted,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> std = sigma_twocomp(predicted,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_saemix@results@respar[1], f_saemix@results@respar[2]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_data <- transform(return_data,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized = residual / std)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- list(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod = object[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mmkin = object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = object[[1]]$solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">226</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transformations = transformations,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">227</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = object[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = object[[1]]$transform_fractions,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = covariates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_models = covariate_models,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sm = m_saemix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">232</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> so = f_saemix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call = call,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = fit_time,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> FIM_failed = FIM_failed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mean_dp_start = attr(m_saemix, "mean_dp_start"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms.fixed = object[[1]]$bparms.fixed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">238</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data = return_data,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod = object[[1]]$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> date.fit = date(),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saemixversion = as.character(utils::packageVersion("saemix")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinversion = as.character(utils::packageVersion("mkin")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Rversion = paste(R.version$major, R.version$minor, sep=".")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">245</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">246</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!fit_failed) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$mkin_ds_order <- mkin_ds_order</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$saemix_ds_order <- saemix_ds_order</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$bparms.optim <- bparms_optim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">251</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- c("saem.mmkin", "mixed.mmkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An saem.mmkin object to print</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">261</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat( "Kinetic nonlinear mixed-effects model fit by SAEM" )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">262</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStructural model:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- x$mmkin[[1]]$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">265</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(nrow(x$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$ds)), "datasets\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">270</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">271</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(x$so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">272</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFit did not terminate successfully\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">273</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">274</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nLikelihood computed by importance sampling\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">275</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll <- try(logLik(x$so, type = "is"), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">276</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(ll, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">277</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Not available\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">278</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> AIC = AIC(x$so, type = "is"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> BIC = BIC(x$so, type = "is"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">282</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> logLik = logLik(x$so, type = "is"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">283</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = " "), digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">284</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">285</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">286</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFitted parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">287</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- parms(x, ci = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">288</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(conf.int, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">289</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">290</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">291</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">292</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">293</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">294</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">295</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An [saemix::SaemixModel] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">296</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">297</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">saemix_model <- function(object, solution_type = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transformations = c("mkin", "saemix"), error_model = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">299</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_start = numeric(),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">300</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance.model = "auto", no_random_effect = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">301</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">302</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = NULL, covariate_models = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">303</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> error.init = numeric(),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">304</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> test_log_parms = FALSE, conf.level = 0.6, verbose = FALSE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">305</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">306</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">307</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">308</td> + <td class="coverage">2346<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkin_model <- object[[1]]$mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">309</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">310</td> + <td class="coverage">2346<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(mkin_model$spec) > 1 & solution_type[1] == "analytical") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">311</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("mkin analytical solutions not supported for more thane one observed variable")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">312</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">313</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">314</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_optim <- mean_degparms(object, test_log_parms = test_log_parms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">315</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na_degparms <- names(which(is.na(degparms_optim)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">316</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(na_degparms) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">317</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("Did not find valid starting values for ", paste(na_degparms, collapse = ", "), "\n",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">318</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "Now trying with test_log_parms = FALSE")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">319</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_optim <- mean_degparms(object, test_log_parms = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">320</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">321</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "saemix") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">322</td> + <td class="coverage">779<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_optim <- backtransform_odeparms(degparms_optim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">323</td> + <td class="coverage">779<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">324</td> + <td class="coverage">779<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">325</td> + <td class="coverage">779<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1]]$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">326</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">327</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_fixed <- object[[1]]$bparms.fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">328</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">329</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transformations are done in the degradation function by default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">330</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # (transformations = "mkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">331</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = rep(0, length(degparms_optim))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">332</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">333</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">334</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed_parm_names <- grep('_0$', names(degparms_fixed), value = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">335</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">336</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_fixed_names <- setdiff(names(degparms_fixed), odeini_fixed_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">337</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_fixed <- degparms_fixed[odeparms_fixed_names]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">338</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">339</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed <- degparms_fixed[odeini_fixed_parm_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">340</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">341</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">342</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">343</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">344</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Model functions with analytical solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">345</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Fixed parameters, use_of_ff = "min" and turning off sinks currently not supported here</pre> + </td> + </tr> + <tr class="never"> + <td class="num">346</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # In general, we need to consider exactly how the parameters in mkinfit were specified,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">347</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # as the parameters are currently mapped by position in these solutions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">348</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sinks <- sapply(mkin_model$spec, function(x) x$sink)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">349</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(odeparms_fixed) == 0 & mkin_model$use_of_ff == "max" & all(sinks)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">350</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Parent only</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">351</td> + <td class="coverage">2242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(mkin_model$spec) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">352</td> + <td class="coverage">1748<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_type <- mkin_model$spec[[1]]$type</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">353</td> + <td class="coverage">1748<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(odeini_fixed) == 1 && !grepl("_bound$", names(odeini_fixed))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">354</td> + <td class="coverage">50<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "saemix") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">355</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("saemix transformations are not supported for parent fits with fixed initial parent value")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">356</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">357</td> + <td class="coverage">50<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "SFO") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">358</td> + <td class="coverage">50<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("saemix needs at least two parameters to work on.")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">359</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">360</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "FOMC") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">361</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">362</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed / (xidep[, "time"]/exp(psi[id, 2]) + 1)^exp(psi[id, 1])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">363</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">364</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">365</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "DFOP") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">366</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">367</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> g <- plogis(psi[id, 3])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">368</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">369</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed * (g * exp(- exp(psi[id, 1]) * t) +</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">370</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> (1 - g) * exp(- exp(psi[id, 2]) * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">371</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">372</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">373</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "HS") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">374</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">375</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> tb <- exp(psi[id, 3])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">376</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">377</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> k1 = exp(psi[id, 1])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">378</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed * ifelse(t <= tb,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">379</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- k1 * t),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">380</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- k1 * tb) * exp(- exp(psi[id, 2]) * (t - tb)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">381</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">382</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">383</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">384</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(odeini_fixed) == 2) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">385</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("SFORB with fixed initial parent value is not supported")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">386</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">387</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "SFO") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">388</td> + <td class="coverage">785<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">389</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">390</td> + <td class="coverage">2628025<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * exp( - exp(psi[id, 2]) * xidep[, "time"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">391</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">392</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">393</td> + <td class="coverage">502<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">394</td> + <td class="coverage">4054103<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * exp( - psi[id, 2] * xidep[, "time"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">395</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">396</td> + <td class="coverage">502<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">397</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">398</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">399</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "FOMC") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">400</td> + <td class="coverage">76<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">401</td> + <td class="coverage">41<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">402</td> + <td class="coverage">510269<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] / (xidep[, "time"]/exp(psi[id, 3]) + 1)^exp(psi[id, 2])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">403</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">404</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">405</td> + <td class="coverage">35<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">406</td> + <td class="coverage">432565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] / (xidep[, "time"]/psi[id, 3] + 1)^psi[id, 2]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">407</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">408</td> + <td class="coverage">35<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">409</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">410</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">411</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "DFOP") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">412</td> + <td class="coverage">677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">413</td> + <td class="coverage">637<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">414</td> + <td class="coverage">8785439<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- plogis(psi[id, 4])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">415</td> + <td class="coverage">8785439<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">416</td> + <td class="coverage">8785439<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * (g * exp(- exp(psi[id, 2]) * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">417</td> + <td class="coverage">8785439<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (1 - g) * exp(- exp(psi[id, 3]) * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">418</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">419</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">420</td> + <td class="coverage">40<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">421</td> + <td class="coverage">507885<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- psi[id, 4]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">422</td> + <td class="coverage">507885<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">423</td> + <td class="coverage">507885<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * (g * exp(- psi[id, 2] * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">424</td> + <td class="coverage">507885<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (1 - g) * exp(- psi[id, 3] * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">425</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">426</td> + <td class="coverage">40<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 1, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">427</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">428</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">429</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "SFORB") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">430</td> + <td class="coverage">150<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">431</td> + <td class="coverage">130<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">432</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_12 <- exp(psi[id, 3])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">433</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_21 <- exp(psi[id, 4])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">434</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_1output <- exp(psi[id, 2])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">435</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">436</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">437</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - k_1output * k_21)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">438</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">439</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">440</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">441</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">442</td> + <td class="coverage">1240580<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">443</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">444</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">445</td> + <td class="coverage">20<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">446</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_12 <- psi[id, 3]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">447</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_21 <- psi[id, 4]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">448</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_1output <- psi[id, 2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">449</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">450</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">451</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - k_1output * k_21)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">452</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">453</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">454</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">455</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">456</td> + <td class="coverage">290980<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">457</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">458</td> + <td class="coverage">20<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 1, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">459</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">460</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">461</td> + <td class="coverage">1698<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "HS") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">462</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">463</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">464</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tb <- exp(psi[id, 4])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">465</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">466</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- exp(psi[id, 2])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">467</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * ifelse(t <= tb,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">468</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- k1 * t),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">469</td> + <td class="coverage">150610<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- k1 * tb) * exp(- exp(psi[id, 3]) * (t - tb)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">470</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">471</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">472</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">473</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> tb <- psi[id, 4]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">474</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">475</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> psi[id, 1] * ifelse(t <= tb,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">476</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- psi[id, 2] * t),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">477</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> exp(- psi[id, 2] * tb) * exp(- psi[id, 3] * (t - tb)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">478</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">479</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 1, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">480</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">481</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">482</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">483</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">484</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">485</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Parent with one metabolite</pre> + </td> + </tr> + <tr class="never"> + <td class="num">486</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Parameter names used in the model functions are as in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">487</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # https://nbviewer.jupyter.org/urls/jrwb.de/nb/Symbolic%20ODE%20solutions%20for%20mkin.ipynb</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">488</td> + <td class="coverage">2192<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> types <- unname(sapply(mkin_model$spec, function(x) x$type))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">489</td> + <td class="coverage">2192<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(mkin_model$spec) == 2 &! "SFORB" %in% types ) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">490</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Initial value for the metabolite (n20) must be fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">491</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (names(odeini_fixed) == names(mkin_model$spec)[2]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">492</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n20 <- odeini_fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">493</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_name <- names(mkin_model$spec)[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">494</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(types, c("SFO", "SFO"))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">495</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">496</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">497</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">498</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 <- psi[id, 1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">499</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- exp(psi[id, 2])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">500</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- exp(psi[id, 3])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">501</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- plogis(psi[id, 4])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">502</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(xidep[, "name"] == parent_name,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">503</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 * exp(- k1 * t),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">504</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">505</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">506</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">507</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">508</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">509</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">510</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">511</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> n10 <- psi[id, 1]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">512</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- psi[id, 2]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">513</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- psi[id, 3]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">514</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- psi[id, 4]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">515</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(xidep[, "name"] == parent_name,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">516</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> n10 * exp(- k1 * t),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">517</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> (((k2 - k1) * n20 - f12 * k1 * n10) * exp(- k2 * t)) / (k2 - k1) +</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">518</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> (f12 * k1 * n10 * exp(- k1 * t)) / (k2 - k1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">519</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">520</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">521</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 1, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">522</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">523</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">524</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(types, c("DFOP", "SFO"))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">525</td> + <td class="coverage">286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">526</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">527</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">528</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 <- psi[id, 1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">529</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- exp(psi[id, 2])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">530</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- plogis(psi[id, 3])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">531</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> l1 <- exp(psi[id, 4])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">532</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> l2 <- exp(psi[id, 5])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">533</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- plogis(psi[id, 6])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">534</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(xidep[, "name"] == parent_name,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">535</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">536</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) -</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">537</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">538</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">539</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((f12 * l1 + (f12 * g - f12) * k2) * l2 -</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">540</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 * g * k2 * l1) * n10) * exp( - k2 * t)) /</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">541</td> + <td class="coverage">1821022<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((l1 - k2) * l2 - k2 * l1 + k2^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">542</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">543</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">544</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">545</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">546</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- xidep[, "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">547</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 <- psi[id, 1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">548</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- psi[id, 2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">549</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- psi[id, 3]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">550</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> l1 <- psi[id, 4]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">551</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> l2 <- psi[id, 5]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">552</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- psi[id, 6]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">553</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(xidep[, "name"] == parent_name,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">554</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 * (g * exp(- l1 * t) + (1 - g) * exp(- l2 * t)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">555</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((f12 * g - f12) * l2 * n10 * exp(- l2 * t)) / (l2 - k2) -</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">556</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (f12 * g * l1 * n10 * exp(- l1 * t)) / (l1 - k2) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">557</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((((l1 - k2) * l2 - k2 * l1 + k2^2) * n20 +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">558</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((f12 * l1 + (f12 * g - f12) * k2) * l2 -</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">559</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 * g * k2 * l1) * n10) * exp( - k2 * t)) /</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">560</td> + <td class="coverage">2908620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((l1 - k2) * l2 - k2 * l1 + k2^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">561</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">562</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">563</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = c(0, 1, 3, 1, 1, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">564</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">565</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">566</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">567</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">568</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">569</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">570</td> + <td class="coverage">2192<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.function(model_function) & solution_type == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">571</td> + <td class="coverage">2083<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "analytical saemix"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">572</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">573</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">574</td> + <td class="coverage">109<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "saemix") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">575</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Using saemix transformations is only supported if an analytical solution is implemented for saemix")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">576</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">577</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">578</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "auto")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">579</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type <- object[[1]]$solution_type</pre> + </td> + </tr> + <tr class="never"> + <td class="num">580</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">581</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define some variables to avoid function calls in model function</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">582</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms_optim_names <- names(degparms_optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">583</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_optim_names <- gsub('_0$', '', odeini_optim_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">584</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diff_names <- names(mkin_model$diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">585</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ode_transparms_optim_names <- setdiff(transparms_optim_names, odeini_optim_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">586</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates <- object[[1]]$transform_rates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">587</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions <- object[[1]]$transform_fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">588</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">589</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get native symbol info for speed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">590</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">591</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "deSolve" & !is.null(mkin_model$cf)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">592</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkin_model$symbols <- try(deSolve::checkDLL(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">593</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dllname = mkin_model$dll_info[["name"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">594</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = "diffs", initfunc = "initpar",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">595</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> jacfunc = NULL, nout = 0, outnames = NULL))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">596</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(mkin_model$symbols, "try-error")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">597</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">598</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">599</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">600</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">601</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define the model function</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">602</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- function(psi, id, xidep) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">603</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">604</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uid <- unique(id)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">605</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">606</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_list <- lapply(uid, function(i) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">607</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">608</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms_optim <- as.numeric(psi[i, ]) # psi[i, ] is a dataframe when called in saemix.predict</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">609</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(transparms_optim) <- transparms_optim_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">610</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">611</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_optim <- transparms_optim[odeini_optim_parm_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">612</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini_optim) <- odeini_optim_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">613</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">614</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- c(odeini_optim, odeini_fixed)[diff_names]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">615</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">616</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">617</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">618</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">619</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- c(odeparms_optim, odeparms_fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">620</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">621</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xidep_i <- xidep[which(id == i), ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">622</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">623</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type[1] == "analytical") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">624</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> out_values <- mkin_model$deg_func(xidep_i, odeini, odeparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">625</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">626</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">627</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> i_time <- xidep_i$time</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">628</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> i_name <- xidep_i$name</pre> + </td> + </tr> + <tr class="never"> + <td class="num">629</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">630</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_wide <- mkinpredict(mkin_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">631</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms = odeparms, odeini = odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">632</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">633</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes = sort(unique(i_time)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">634</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na_stop = FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">635</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">636</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">637</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_index <- cbind(as.character(i_time), as.character(i_name))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">638</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_values <- out_wide[out_index]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">639</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">640</td> + <td class="coverage">43671888<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(out_values)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">641</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">642</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- unlist(res_list)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">643</td> + <td class="coverage">873912<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">644</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">645</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">646</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">647</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(error_model, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">648</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model = object[[1]]$err_mod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">649</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">650</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error.model <- switch(error_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">651</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "constant",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">652</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = "combined",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">653</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = "constant")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">654</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">655</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model == "obs") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">656</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("The error model 'obs' (variance by variable) can currently not be transferred to an saemix model")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">657</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">658</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">659</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_psi0 <- degparms_optim</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">660</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_psi0[names(degparms_start)] <- degparms_start</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">661</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi0_matrix <- matrix(degparms_psi0, nrow = 1,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">662</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list("(Intercept)", names(degparms_psi0)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">663</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">664</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (covariance.model[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">665</td> + <td class="coverage">2062<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance_diagonal <- rep(1, length(degparms_optim))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">666</td> + <td class="coverage">2062<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(no_random_effect)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">667</td> + <td class="coverage">766<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_no_random <- which(names(degparms_psi0) %in% no_random_effect)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">668</td> + <td class="coverage">766<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance_diagonal[degparms_no_random] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">669</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">670</td> + <td class="coverage">2062<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance.model = diag(covariance_diagonal)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">671</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">672</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">673</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (omega.init[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">674</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">675</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_eta_ini <- as.numeric( # remove names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">676</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mean_degparms(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">677</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> random = TRUE, test_log_parms = TRUE)$eta)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">678</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">679</td> + <td class="coverage">1413<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init <- 2 * diag(degparms_eta_ini^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">680</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">681</td> + <td class="coverage">774<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init <- matrix(nrow = 0, ncol = 0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">682</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">683</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">684</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">685</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(covariate_models)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">686</td> + <td class="coverage">2027<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate.model <- matrix(nrow = 0, ncol = 0) # default in saemixModel()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">687</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">688</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_dependent <- sapply(covariate_models, function(x) as.character(x[[2]]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">689</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates_in_models = unique(unlist(lapply(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">690</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_models, function(x)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">691</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(attr(terms(x), "factors"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">692</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">693</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates_not_available <- setdiff(covariates_in_models, names(covariates))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">694</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(covariates_not_available) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">695</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Covariate(s) ", paste(covariates_not_available, collapse = ", "),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">696</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> " used in the covariate models not available in the covariate data")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">697</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">698</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi0_matrix <- rbind(psi0_matrix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">699</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> matrix(0, nrow = length(covariates), ncol = ncol(psi0_matrix),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">700</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(names(covariates), colnames(psi0_matrix))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">701</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate.model <- matrix(0, nrow = length(covariates),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">702</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ncol = ncol(psi0_matrix),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">703</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">704</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = names(covariates),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">705</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms = colnames(psi0_matrix)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">706</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformations == "saemix") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">707</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Covariate models with saemix transformations currently not supported")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">708</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">709</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_trans <- as.data.frame(t(sapply(object, parms, transformed = TRUE)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">710</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (covariate_model in covariate_models) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">711</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_name <- as.character(covariate_model[[2]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">712</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_data <- cbind(parms_trans, covariates)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">713</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ini_model <- lm(covariate_model, data = model_data)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">714</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ini_coef <- coef(ini_model)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">715</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi0_matrix[names(ini_coef), covariate_name] <- ini_coef</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">716</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate.model[names(ini_coef)[-1], covariate_name] <- as.numeric(as.logical(ini_coef[-1]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">717</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">718</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">719</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">720</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- saemix::saemixModel(model_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">721</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi0 = psi0_matrix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">722</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Mixed model generated from mmkin object",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">723</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform.par = transform.par,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">724</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error.model = error.model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">725</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> verbose = verbose,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">726</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariance.model = covariance.model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">727</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate.model = covariate.model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">728</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> omega.init = omega.init,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">729</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error.init = error.init,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">730</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">731</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">732</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(res, "mean_dp_start") <- degparms_optim</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">733</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">734</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">735</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">736</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">737</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom rlang !!!</pre> + </td> + </tr> + <tr class="never"> + <td class="num">738</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An [saemix::SaemixData] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">739</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">740</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">saemix_data <- function(object, covariates = NULL, verbose = FALSE, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">741</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">742</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_names <- colnames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">743</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">744</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">745</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds_list) <- ds_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">746</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_saemix_all <- vctrs::vec_rbind(!!!ds_list, .names_to = "ds")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">747</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_saemix <- data.frame(ds = ds_saemix_all$ds,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">748</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name = as.character(ds_saemix_all$variable),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">749</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = ds_saemix_all$time,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">750</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> value = ds_saemix_all$observed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">751</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stringsAsFactors = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">752</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(covariates)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">753</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.covariates <- names(covariates)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">754</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates$ds <- rownames(covariates)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">755</td> + <td class="coverage">160<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_saemix <- merge(ds_saemix, covariates, sort = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">756</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">757</td> + <td class="coverage">2027<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.covariates <- character(0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">758</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">759</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">760</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- saemix::saemixData(ds_saemix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">761</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.group = "ds",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">762</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.predictors = c("time", "name"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">763</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.response = "value",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">764</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name.covariates = name.covariates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">765</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> verbose = verbose,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">766</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">767</td> + <td class="coverage">2187<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">768</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">769</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">770</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' logLik method for saem.mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">771</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">772</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The fitted [saem.mmkin] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">773</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Passed to [saemix::logLik.SaemixObject]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">774</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method Passed to [saemix::logLik.SaemixObject]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">775</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">776</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">logLik.saem.mmkin <- function(object, ..., method = c("is", "lin", "gq")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">777</td> + <td class="coverage">4404<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method <- match.arg(method)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">778</td> + <td class="coverage">4404<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(logLik(object$so, method = method))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">779</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">780</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">781</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">782</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.saem.mmkin <- function(object, ..., evaluate = TRUE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">783</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- object$call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">784</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # For some reason we get saem.mmkin in the call when using mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">785</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # so we need to fix this so we do not have to export saem.mmkin in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">786</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # addition to the S3 method</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">787</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[1]] <- saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">788</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">789</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We also need to provide the mmkin object in the call, so it</pre> + </td> + </tr> + <tr class="never"> + <td class="num">790</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # will also be found when called by testthat or pkgdown</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">791</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[2]] <- object$mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">792</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">793</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments <- match.call(expand.dots = FALSE)$...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">794</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">795</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(update_arguments) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">796</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_in_call <- !is.na(match(names(update_arguments), names(call)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">797</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">798</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">799</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (a in names(update_arguments)[update_arguments_in_call]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">800</td> + <td class="coverage">35<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[a]] <- update_arguments[[a]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">801</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">802</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">803</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_not_in_call <- !update_arguments_in_call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">804</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(any(update_arguments_not_in_call)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">805</td> + <td class="coverage">472<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- c(as.list(call), update_arguments[update_arguments_not_in_call])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">806</td> + <td class="coverage">472<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- as.call(call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">807</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">808</td> + <td class="coverage">507<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(evaluate) eval(call, parent.frame())</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">809</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">810</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">811</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">812</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">813</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname parms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">814</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ci Should a matrix with estimates and confidence interval boundaries</pre> + </td> + </tr> + <tr class="never"> + <td class="num">815</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be returned? If FALSE (default), a vector of estimates is returned if no</pre> + </td> + </tr> + <tr class="never"> + <td class="num">816</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' covariates are given, otherwise a matrix of estimates is returned, with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">817</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' each column corresponding to a row of the data frame holding the covariates</pre> + </td> + </tr> + <tr class="never"> + <td class="num">818</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariates A data frame holding covariate values for which to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">819</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' return parameter values. Only has an effect if 'ci' is FALSE.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">820</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parms.saem.mmkin <- function(object, ci = FALSE, covariates = NULL, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">821</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cov.mod <- object$sm@covariance.model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">822</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_cov_mod_parms <- sum(cov.mod[upper.tri(cov.mod, diag = TRUE)])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">823</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_parms <- length(object$sm@name.modpar) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">824</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_cov_mod_parms +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">825</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(object$sm@name.sigma)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">826</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">827</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object$so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">828</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- matrix(rep(NA, 3 * n_parms), ncol = 3)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">829</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(conf.int) <- c("estimate", "lower", "upper")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">830</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">831</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- object$so@results@conf.int[c("estimate", "lower", "upper")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">832</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(conf.int) <- object$so@results@conf.int[["name"]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">833</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int.var <- grepl("^Var\\.", rownames(conf.int))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">834</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- conf.int[!conf.int.var, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">835</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int.cov <- grepl("^Cov\\.", rownames(conf.int))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">836</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- conf.int[!conf.int.cov, ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">837</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">838</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> estimate <- conf.int[, "estimate"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">839</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">840</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(estimate) <- rownames(conf.int)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">841</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">842</td> + <td class="coverage">2904<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ci) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">843</td> + <td class="coverage">1034<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(conf.int)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">844</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">845</td> + <td class="coverage">1870<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(covariates)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">846</td> + <td class="coverage">1760<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(estimate)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">847</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">848</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> est_for_cov <- matrix(NA,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">849</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nrow = length(object$sm@name.modpar), ncol = nrow(covariates),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">850</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = (list(object$sm@name.modpar, rownames(covariates))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">851</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covmods <- object$covariate_models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">852</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(covmods) <- sapply(covmods, function(x) as.character(x[[2]]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">853</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (deg_parm_name in rownames(est_for_cov)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">854</td> + <td class="coverage">440<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (deg_parm_name %in% names(covmods)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">855</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate <- covmods[[deg_parm_name]][[3]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">856</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> beta_degparm_name <- paste0("beta_", covariate,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">857</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "(", deg_parm_name, ")")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">858</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> est_for_cov[deg_parm_name, ] <- estimate[deg_parm_name] +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">859</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates[[covariate]] * estimate[beta_degparm_name]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">860</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">861</td> + <td class="coverage">330<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> est_for_cov[deg_parm_name, ] <- estimate[deg_parm_name]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">862</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">863</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">864</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(est_for_cov)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">865</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">866</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">867</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/status.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Method to get status information for fit array objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The object to investigate</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x The object to be printed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For potential future extensions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object with the same dimensions as the fit array</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' suitable printing method.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">status <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">11</td> + <td class="coverage">589<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("status", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname status</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c("SFO", "FOMC"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list("FOCUS A" = FOCUS_2006_A,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "FOCUS B" = FOCUS_2006_C),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' status(fits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">status.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">26</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_summary_warnings <- character()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sww <- 0 # Counter for Shapiro-Wilks warnings</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(fit) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">31</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit, "try-error")) return("E")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">4391<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sw <- fit$summary_warnings</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">4391<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> swn <- names(sw)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">4391<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(sw) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">35</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(grepl("S", swn))) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">36</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> sww <<- sww + 1</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">37</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> swn <- gsub("S", paste0("S", sww), swn)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">39</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warnstring <- paste(swn, collapse = ", ")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">40</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> names(sw) <- swn</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">41</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> all_summary_warnings <<- c(all_summary_warnings, sw)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">42</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(warnstring)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">4391<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return("OK")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(result) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(result) <- dimnames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> u_swn <- unique(names(all_summary_warnings))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(result, "unique_warnings") <- all_summary_warnings[u_swn]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "status.mmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname status</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.status.mmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> u_w <- attr(x, "unique_warnings")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(x, "unique_warnings") <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x, quote = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in seq_along(u_w)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">66</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat(names(u_w)[i], ": ", u_w[i], "\n", sep = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">376<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "OK")) cat("OK: No warnings\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">69</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "E")) cat("E: Error\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname status</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">status.mhmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object[[1]], "saem.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> test_func <- function(fit) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">78</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return("E")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit$so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">81</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return("E")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(fit$FIM_failed)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">84</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return_values <- c("fixed effects" = "Fth",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">85</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "random effects and error model parameters" = "FO")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">86</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(paste(return_values[fit$FIM_failed], collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return("OK")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">94</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Only mhmkin objects containing saem.mmkin objects currently supported")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object, test_func)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(result) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(result) <- dimnames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "status.mhmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname status</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.status.mhmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x, quote = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "OK")) cat("OK: Fit terminated successfully\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">112</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "Fth")) cat("Fth: Could not invert FIM for fixed effects\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">113</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "FO")) cat("FO: Could not invert FIM for random effects and error model parameters\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">114</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "Fth, FO")) cat("Fth, FO: Could not invert FIM for fixed effects, nor for random effects and error model parameters\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">115</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "E")) cat("E: Error\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/endpoints.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to calculate endpoints for further use from kinetic models fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' with mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function calculates DT50 and DT90 values as well as formation fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from kinetic models fitted with mkinfit. If the SFORB model was specified</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for one of the parents or metabolites, the Eigenvalues are returned. These</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are equivalent to the rate constants of the DFOP model, but with the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' advantage that the SFORB model can also be used for metabolites.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fit An object of class [mkinfit], [nlme.mmkin] or [saem.mmkin], or</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' another object that has list components mkinmod containing an [mkinmod]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation model, and two numeric vectors, bparms.optim and bparms.fixed,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' that contain parameter values for that model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariates Numeric vector with covariate values for all variables in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' any covariate models in the object. If given, it overrides 'covariate_quantile'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariate_quantile This argument only has an effect if the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' object has covariate models. If so, the default is to show endpoints</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for the median of the covariate values (50th percentile).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats optimize</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list with a matrix of dissipation times named distimes, and, if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' applicable, a vector of formation fractions named ff and, if the SFORB model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' was in use, a vector of eigenvalues of these SFORB models, equivalent to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' DFOP rate constants</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note The function is used internally by [summary.mkinfit],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [summary.nlme.mmkin] and [summary.saem.mmkin].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_2 <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(fit_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_3 <- mkinfit("SFORB", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(fit_3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">endpoints <- function(fit, covariates = NULL, covariate_quantile = 0.5) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod <- fit$mkinmod</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- names(mkinmod$spec)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(fit$covariate_models)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(covariates)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = as.data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> apply(fit$covariates, 2, quantile,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_quantile, simplify = FALSE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">52</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_m <- matrix(covariates, byrow = TRUE)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">53</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(covariate_m) <- names(covariates)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">54</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covariate_m) <- "User"</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">55</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> covariates <- as.data.frame(covariate_m)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_trans <- parms(fit, covariates = covariates)[, 1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit, "saem.mmkin") & (fit$transformations == "saemix")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">59</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- degparms_trans</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- backtransform_odeparms(degparms_trans,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = fit$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">110<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = fit$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">56098<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- c(fit$bparms.optim, fit$bparms.fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set up object to return</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep <- list()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$covariates <- covariates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$SFORB <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes <- data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = rep(NA, length(obs_vars)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = rep(NA, length(obs_vars)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> type = names(mkinmod$map[[obs_var]])[1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get formation fractions if directly fitted, and calculate remaining fraction to sink</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names = grep(paste("^f", obs_var, sep = "_"), names(degparms), value=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(f_names) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_values = degparms[f_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_to_sink = 1 - sum(f_values)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(f_to_sink) = ifelse(type == "SFORB",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(obs_var, "free", "sink", sep = "_"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(obs_var, "sink", sep = "_"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (f_name in f_names) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">17338<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff[[sub("f_", "", sub("_to_", "_", f_name))]] = f_values[[f_name]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">15068<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff = append(ep$ff, f_to_sink)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the rest</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "SFO") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">40900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_names = grep(paste("^k", obs_var, sep="_"), names(degparms), value=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">40900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_tot = sum(degparms[k_names])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">40900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = log(2)/k_tot</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">40900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = log(10)/k_tot</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">40900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod$use_of_ff == "min" && length(obs_vars) > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">622<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (k_name in k_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">932<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff[[sub("k_", "", k_name)]] = degparms[[k_name]] / k_tot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "FOMC") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> alpha = degparms["alpha"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> beta = degparms["beta"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = beta * (2^(1/alpha) - 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = beta * (10^(1/alpha) - 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">1790<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50back")] = DT50_back</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "IORE") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_names = grep(paste("^k__iore", obs_var, sep="_"), names(degparms), value=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_tot = sum(degparms[k_names])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # From the NAFTA kinetics guidance, p. 5</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n = degparms[paste("N", obs_var, sep = "_")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k = k_tot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Use the initial concentration of the parent compound</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> source_name = mkinmod$map[[1]][[1]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c0 = degparms[paste(source_name, "0", sep = "_")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> alpha = 1 / (n - 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> beta = (c0^(1 - n))/(k * (n - 1))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = beta * (2^(1/alpha) - 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = beta * (10^(1/alpha) - 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50back")] = DT50_back</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod$use_of_ff == "min") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">134</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (k_name in k_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">136</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff[[sub("k_", "", k_name)]] = degparms[[k_name]] / k_tot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "DFOP") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 = degparms["k1"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 = degparms["k2"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g = degparms["g"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f <- function(log_t, x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">684705<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t <- exp(log_t)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">684705<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fraction <- g * exp( - k1 * t) + (1 - g) * exp( - k2 * t)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">684705<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (fraction - (1 - x/100))^2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_k1 = log(2)/k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_k2 = log(2)/k2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90_k1 = log(10)/k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90_k2 = log(10)/k2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 <- try(exp(optimize(f, c(log(DT50_k1), log(DT50_k2)), x=50)$minimum),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 <- try(exp(optimize(f, c(log(DT90_k1), log(DT90_k2)), x=90)$minimum),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> silent = TRUE)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">158</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(DT50, "try-error")) DT50 = NA</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">159</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(DT90, "try-error")) DT90 = NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50back")] = DT50_back</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_k1")] = DT50_k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">27729<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_k2")] = DT50_k2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "HS") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 = degparms["k1"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 = degparms["k2"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tb = degparms["tb"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DTx <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">636<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DTx.a <- (log(100/(100 - x)))/k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">636<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DTx.b <- tb + (log(100/(100 - x)) - k1 * tb)/k2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">339<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (DTx.a < tb) DTx <- DTx.a</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">297<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else DTx <- DTx.b</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">636<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(DTx)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 <- DTx(50)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 <- DTx(90)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_k1 = log(2)/k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_k2 = log(2)/k2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50back")] = DT50_back</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_k1")] = DT50_k1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">318<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_k2")] = DT50_k2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "SFORB") {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # FOCUS kinetics (2006), p. 60 f</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_out_names = grep(paste("^k", obs_var, "free", sep="_"), names(degparms), value=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_out_names = setdiff(k_out_names, paste("k", obs_var, "free", "bound", sep="_"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_1output = sum(degparms[k_out_names])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_12 = degparms[paste("k", obs_var, "free", "bound", sep="_")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_21 = degparms[paste("k", obs_var, "bound", "free", sep="_")]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - k_1output * k_21)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g = (k_12 + k_21 - b1)/(b2 - b1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_b1 = log(2)/b1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_b2 = log(2)/b2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90_b1 = log(10)/b1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90_b2 = log(10)/b2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFORB_fraction = function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">60096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g * exp(-b1 * t) + (1 - g) * exp(-b2 * t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_50 <- function(log_t) (SFORB_fraction(exp(log_t)) - 0.5)^2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> log_DT50 <- try(optimize(f_50, c(log(DT50_b1), log(DT50_b2)))$minimum,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_90 <- function(log_t) (SFORB_fraction(exp(log_t)) - 0.1)^2</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> log_DT90 <- try(optimize(f_90, c(log(DT90_b1), log(DT90_b2)))$minimum,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> silent = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">215</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = if (inherits(log_DT50, "try-error")) NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else exp(log_DT50)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = if (inherits(log_DT90, "try-error")) NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else exp(log_DT90)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">220</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_back = DT90 / (log(10)/log(2)) # Backcalculated DT50 as recommended in FOCUS 2011</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (k_out_name in k_out_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">223</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">2618<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$ff[[sub("k_", "", k_out_name)]] = degparms[[k_out_name]] / k_1output</pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Return the eigenvalues for comparison with DFOP rate constants</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Return g for comparison with DFOP</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$SFORB[[paste(obs_var, "g", sep="_")]] = g</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50back")] = DT50_back</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c(paste("DT50", obs_var, "b1", sep = "_"))] = DT50_b1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">2616<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c(paste("DT50", obs_var, "b2", sep = "_"))] = DT50_b2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "logistic") {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # FOCUS kinetics (2014) p. 67</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> kmax = degparms["kmax"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k0 = degparms["k0"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> r = degparms["r"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50 = (1/r) * log(1 - ((kmax/k0) * (1 - 2^(r/kmax))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT90 = (1/r) * log(1 - ((kmax/k0) * (1 - 10^(r/kmax))))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_k0 = log(2)/k0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">246</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DT50_kmax = log(2)/kmax</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_k0")] = DT50_k0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50_kmax")] = DT50_kmax</pre> + </td> + </tr> + <tr class="never"> + <td class="num">249</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">250</td> + <td class="coverage">73858<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">251</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">38846<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$ff) == 0) ep$ff <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">53592<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$SFORB) == 0) ep$SFORB <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">254</td> + <td class="coverage">56208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ep)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinmod.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to set up a kinetic model with one or more state variables</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function is usually called using a call to [mkinsub()] for each observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variable, specifying the corresponding submodel as well as outgoing pathways</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (see examples).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' For the definition of model types and their parameters, the equations given</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in the FOCUS and NAFTA guidance documents are used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' For kinetic models with more than one observed variable, a symbolic solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the system of differential equations is included in the resulting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinmod object in some cases, speeding up the solution.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If a C compiler is found by [pkgbuild::has_compiler()] and there</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is more than one observed variable in the specification, C code is generated</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for evaluating the differential equations, compiled using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [inline::cfunction()] and added to the resulting mkinmod object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ... For each observed variable, a list as obtained by [mkinsub()]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' has to be specified as an argument (see examples). Currently, single</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' first order kinetics "SFO", indeterminate order rate equation kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "IORE", or single first order with reversible binding "SFORB" are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' implemented for all variables, while "FOMC", "DFOP", "HS" and "logistic"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' can additionally be chosen for the first variable which is assumed to be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the source compartment.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Additionally, [mkinsub()] has an argument \code{to}, specifying names of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables to which a transfer is to be assumed in the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If the argument \code{use_of_ff} is set to "min"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and the model for the compartment is "SFO" or "SFORB", an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' additional [mkinsub()] argument can be \code{sink = FALSE}, effectively</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fixing the flux to sink to zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' In print.mkinmod, this argument is currently not used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param use_of_ff Specification of the use of formation fractions in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model equations and, if applicable, the coefficient matrix. If "max",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' formation fractions are always used (default). If "min", a minimum use of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' formation fractions is made, i.e. each first-order pathway to a metabolite</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' has its own rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param speclist The specification of the observed variables and their</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' submodel types and pathways can be given as a single list using this</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' argument. Default is NULL.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param quiet Should messages be suppressed?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose If \code{TRUE}, passed to [inline::cfunction()] if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' applicable to give detailed information about the C function being built.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param name A name for the model. Should be a valid R object name.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param dll_dir Directory where an DLL object, if generated internally by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [inline::cfunction()], should be saved. The DLL will only be stored in a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' permanent location for use in future sessions, if 'dll_dir' and 'name'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are specified. This is helpful if fit objects are cached e.g. by knitr,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as the cache remains functional across sessions if the DLL is stored in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a user defined location.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param unload If a DLL from the target location in 'dll_dir' is already</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loaded, should that be unloaded first?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param overwrite If a file exists at the target DLL location in 'dll_dir',</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' should this be overwritten?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom methods signature</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list of class \code{mkinmod} for use with [mkinfit()],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' containing, among others,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{diffs}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A vector of string representations of differential equations, one for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' each modelling variable.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{map}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A list containing named character vectors for each observed variable,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' specifying the modelling variables by which it is represented.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{use_of_ff}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The content of \code{use_of_ff} is passed on in this list component.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{deg_func}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If generated, a function containing the solution of the degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{coefmat}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The coefficient matrix, if the system of differential equations can be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' represented by one.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{cf}{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If generated, a compiled function calculating the derivatives as</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' returned by cfunction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note The IORE submodel is not well tested for metabolites. When using this</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model for metabolites, you may want to read the note in the help</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' page to [mkinfit].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' NAFTA Technical Working Group on Pesticides (not dated) Guidance for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Evaluating and Calculating Degradation Kinetics in Environmental Media</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO <- mkinmod(parent = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # One parent compound, one metabolite, both single first order</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(SFO_SFO)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Now supplying compound names used for plotting, and write to user defined location</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We need to choose a path outside the session tempdir because this gets removed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' DLL_dir <- "~/.local/share/mkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (!dir.exists(DLL_dir)) dir.create(DLL_dir)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO.2 <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", "m1", full_name = "Test compound"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO", full_name = "Metabolite M1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' name = "SFO_SFO", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Now we can save the model and restore it in a new session</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' saveRDS(SFO_SFO.2, file = "~/SFO_SFO.rds")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Terminate the R session here if you would like to check, and then do</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(mkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO.3 <- readRDS("~/SFO_SFO.rds")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = "deSolve")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Show details of creating the C function</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"), verbose = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The symbolic solution which is available in this case is not</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # made for human reading but for speed of computation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO$deg_func</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # If we have several parallel metabolites</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_DFOP_par <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("DFOP", c("M1", "M2")),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' synthetic_data_for_UBA_2014[[12]]$data,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinmod <- function(..., use_of_ff = "max", name = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> speclist = NULL, quiet = FALSE, verbose = FALSE, dll_dir = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> unload = FALSE, overwrite = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">4940<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(speclist)) spec <- list(...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">3905<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else spec <- speclist</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">8845<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- names(spec)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">8845<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> save_msg <- "You need to specify both 'name' and 'dll_dir' to save a model DLL"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">8845<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(dll_dir)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">155</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!dir.exists(dll_dir)) stop(dll_dir, " does not exist")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">156</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(name)) stop(save_msg)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check if any of the names of the observed variables contains any other</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">8845<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(grep(obs_var, obs_vars)) > 1) stop("Sorry, variable names can not contain each other")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (grepl("_to_", obs_var)) stop("Sorry, names of observed variables can not contain _to_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (obs_var == "sink") stop("Naming a compound 'sink' is not supported")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">8533<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!use_of_ff %in% c("min", "max"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The use of formation fractions 'use_of_ff' can only be 'min' or 'max'")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">8429<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- vector()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # }}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not return a coefficient matrix mat when FOMC, IORE, DFOP, HS or logistic is used for the parent {{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">8429<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS", "logistic")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">2280<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mat = FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">6149<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> } else mat = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Establish a list of differential equations as well as a map from observed {{{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # compartments to differential equations</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">8429<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">8429<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> map <- list()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">8429<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (varname in obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">183</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check the type component of the compartment specification {{{</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">185</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if(is.null(spec[[varname]]$type)) stop(</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">186</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "Every part of the model specification must be a list containing a type component")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB", "logistic")) stop(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Available types are SFO, FOMC, IORE, DFOP, HS, SFORB and logistic only")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">13150<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS", "logistic") & match(varname, obs_vars) != 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop(paste("Types FOMC, DFOP, HS and logistic are only implemented for the first compartment,",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "which is assumed to be the source compartment"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">192</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # New (sub)compartments (boxes) needed for the model type {{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> new_boxes <- switch(spec[[varname]]$type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFO = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> FOMC = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> IORE = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DFOP = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> HS = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> logistic = varname,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFORB = paste(varname, c("free", "bound"), sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> map[[varname]] <- new_boxes</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(map[[varname]]) <- rep(spec[[varname]]$type, length(new_boxes)) #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Start a new differential equation for each new box {{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> new_diffs <- paste("d_", new_boxes, " =", sep = "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(new_diffs) <- new_boxes</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">13046<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- c(diffs, new_diffs) #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Create content of differential equations and build parameter list {{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">8221<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (varname in obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the name of the box(es) we are working on for the decline term(s)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">12838<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> box_1 = map[[varname]][[1]] # This is the only box unless type is SFORB</pre> + </td> + </tr> + <tr class="never"> + <td class="num">217</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Turn on sink if this is not explicitly excluded by the user by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # specifying sink=FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(is.null(spec[[varname]]$sink)) spec[[varname]]$sink <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">220</td> + <td class="coverage">12838<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type %in% c("SFO", "IORE", "SFORB")) { # {{{ Add decline term</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">10838<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (use_of_ff == "min") { # Minimum use of formation fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">1304<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "IORE" && length(spec[[varname]]$to) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Transformation reactions from compounds modelled with IORE\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "are only supported with formation fractions (use_of_ff = 'max')")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">226</td> + <td class="coverage">1200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$sink) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # If sink is requested, add first-order/IORE sink term</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_compound_sink <- paste("k", box_1, "sink", sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "IORE") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">230</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> k_compound_sink <- paste("k__iore", box_1, "sink", sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">232</td> + <td class="coverage">952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, k_compound_sink)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste(k_compound_sink, "*", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "IORE") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">235</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> N <- paste("N", box_1, sep = "_")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">236</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, N)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">237</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste0(decline_term, "^", N)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">239</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # otherwise no decline term needed here</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">248<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term = "0"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # Maximum use of formation fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">9534<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_compound <- paste("k", box_1, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">244</td> + <td class="coverage">9534<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "IORE") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_compound <- paste("k__iore", box_1, sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">9534<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, k_compound)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">9534<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste(k_compound, "*", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">9534<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "IORE") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">250</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N <- paste("N", box_1, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, N)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste0(decline_term, "^", N)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">253</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">256</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "FOMC") { # {{{ Add FOMC decline term</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # From p. 53 of the FOCUS kinetics report, without the power function so it works in C</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">258</td> + <td class="coverage">381<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste("(alpha/beta) * 1/((time/beta) + 1) *", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">259</td> + <td class="coverage">381<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, "alpha", "beta")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">261</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "DFOP") { # {{{ Add DFOP decline term</pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # From p. 57 of the FOCUS kinetics report</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">1283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">1283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, "k1", "k2", "g")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> HS_decline <- "ifelse(time <= tb, k1, k2)" # Used below for automatic translation to C</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "HS") { # {{{ Add HS decline term</pre> + </td> + </tr> + <tr class="never"> + <td class="num">268</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # From p. 55 of the FOCUS kinetics report</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">30<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste(HS_decline, "*", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">270</td> + <td class="coverage">30<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, "k1", "k2", "tb")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "logistic") { # {{{ Add logistic decline term</pre> + </td> + </tr> + <tr class="never"> + <td class="num">273</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # From p. 67 of the FOCUS kinetics report (2014)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">274</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term <- paste("(k0 * kmax)/(k0 + (kmax - k0) * exp(-r * time)) *", box_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">275</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, "kmax", "k0", "r")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">276</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">277</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[box_1]] <- paste(diffs[[box_1]], "-", decline_term)#}}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> box_2 = map[[varname]][[2]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_free_bound <- paste("k", varname, "free", "bound", sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">282</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_bound_free <- paste("k", varname, "bound", "free", sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">283</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, k_free_bound, k_bound_free)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> reversible_binding_term_1 <- paste("-", k_free_bound, "*", box_1, "+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_bound_free, "*", box_2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">286</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> reversible_binding_term_2 <- paste("+", k_free_bound, "*", box_1, "-",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">287</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_bound_free, "*", box_2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">288</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[box_1]] <- paste(diffs[[box_1]], reversible_binding_term_1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">289</td> + <td class="coverage">25<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[box_2]] <- paste(diffs[[box_2]], reversible_binding_term_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">290</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">291</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">292</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transfer between compartments#{{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">293</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> to <- spec[[varname]]$to</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">294</td> + <td class="coverage">12734<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(!is.null(to)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">295</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Name of box from which transfer takes place</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">296</td> + <td class="coverage">4174<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> origin_box <- box_1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">297</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Number of targets</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">299</td> + <td class="coverage">4174<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_targets = length(to)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">300</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">301</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Add transfer terms to listed compartments</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">302</td> + <td class="coverage">4174<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (target in to) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">303</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!target %in% obs_vars) stop("You did not specify a submodel for target variable ", target)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">304</td> + <td class="coverage">4813<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> target_box <- switch(spec[[target]]$type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">305</td> + <td class="coverage">4813<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFO = target,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">306</td> + <td class="coverage">4813<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> IORE = target,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">307</td> + <td class="coverage">4813<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFORB = paste(target, "free", sep = "_"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">308</td> + <td class="coverage">4813<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (use_of_ff == "min" && spec[[varname]]$type %in% c("SFO", "SFORB"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">309</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">310</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_from_to <- paste("k", origin_box, target_box, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">311</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, k_from_to)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">312</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[origin_box]] <- paste(diffs[[origin_box]], "-",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">313</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_from_to, "*", origin_box)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">314</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[target_box]] <- paste(diffs[[target_box]], "+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">315</td> + <td class="coverage">601<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_from_to, "*", origin_box)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">316</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">317</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not introduce a formation fraction if this is the only target</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">318</td> + <td class="coverage">4212<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (spec[[varname]]$sink == FALSE && n_targets == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">319</td> + <td class="coverage">689<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[target_box]] <- paste(diffs[[target_box]], "+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">320</td> + <td class="coverage">689<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> decline_term)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">321</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">322</td> + <td class="coverage">3523<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fraction_to_target = paste("f", origin_box, "to", target, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">323</td> + <td class="coverage">3523<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(parms, fraction_to_target)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">324</td> + <td class="coverage">3523<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[[target_box]] <- paste(diffs[[target_box]], "+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">325</td> + <td class="coverage">3523<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fraction_to_target, "*", decline_term)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">326</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">327</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">328</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">329</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">330</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } #}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">331</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">332</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model <- list(diffs = diffs, parms = parms, map = map, spec = spec, use_of_ff = use_of_ff, name = name)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">333</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">334</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Create coefficient matrix if possible #{{{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">335</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mat) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">336</td> + <td class="coverage">5941<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> boxes <- names(diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">337</td> + <td class="coverage">5941<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n <- length(boxes)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">338</td> + <td class="coverage">5941<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m <- matrix(nrow=n, ncol=n, dimnames=list(boxes, boxes))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">339</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">340</td> + <td class="coverage">5941<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (use_of_ff == "min") { # {{{ Minimum use of formation fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">341</td> + <td class="coverage">600<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (from in boxes) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">342</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (to in boxes) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">343</td> + <td class="coverage">2405<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (from == to) { # diagonal elements</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">344</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", from, c(boxes, "sink"), sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">345</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = sub("free.*bound", "free_bound", k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">346</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = sub("bound.*free", "bound_free", k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">347</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.effective = intersect(model$parms, k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">348</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[from,to] = ifelse(length(k.effective) > 0,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">349</td> + <td class="coverage">1201<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste("-", k.effective, collapse = " "), "0")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">350</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">351</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # off-diagonal elements</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">352</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", from, to, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">353</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (sub("_free$", "", from) == sub("_bound$", "", to)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">354</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", sub("_free$", "_free_bound", from), sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">355</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">356</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (sub("_bound$", "", from) == sub("_free$", "", to)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">357</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", sub("_bound$", "_bound_free", from), sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">358</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">359</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.effective = intersect(model$parms, k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">360</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[to, from] = ifelse(length(k.effective) > 0,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">361</td> + <td class="coverage">1204<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.effective, "0")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">362</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">363</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">364</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } # }}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">365</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # {{{ Use formation fractions where possible</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">366</td> + <td class="coverage">5341<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (from in boxes) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">367</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (to in boxes) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">368</td> + <td class="coverage">15220<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (from == to) { # diagonal elements</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">369</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", from, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">370</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[from,to] = ifelse(k.candidate %in% model$parms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">371</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste("-", k.candidate), "0")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">372</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(grepl("_free", from)) { # add transfer to bound compartment for SFORB</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">373</td> + <td class="coverage">24<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[from,to] = paste(m[from,to], "-", paste("k", from, "bound", sep = "_"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">374</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">375</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(grepl("_bound", from)) { # add backtransfer to free compartment for SFORB</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">376</td> + <td class="coverage">24<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[from,to] = paste("- k", from, "free", sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">377</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">378</td> + <td class="coverage">8074<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[from,to] = m[from,to]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">379</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # off-diagonal elements</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">380</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f.candidate = paste("f", from, "to", to, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">381</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = paste("k", from, to, sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">382</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = sub("free.*bound", "free_bound", k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">383</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k.candidate = sub("bound.*free", "bound_free", k.candidate)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">384</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[to, from] = ifelse(f.candidate %in% model$parms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">385</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(f.candidate, " * k_", from, sep = ""),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">386</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(k.candidate %in% model$parms, k.candidate, "0"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">387</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Special case: singular pathway and no sink</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">388</td> + <td class="coverage">7146<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (spec[[from]]$sink == FALSE && length(spec[[from]]$to) == 1 && to %in% spec[[from]]$to) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">389</td> + <td class="coverage">689<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> m[to, from] = paste("k", from, sep = "_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">390</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">391</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">392</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">393</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">394</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } # }}}</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">395</td> + <td class="coverage">5941<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model$coefmat <- m</pre> + </td> + </tr> + <tr class="never"> + <td class="num">396</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }#}}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">397</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">398</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Try to create a function compiled from C code if there is more than one observed variable {{{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">399</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and a compiler is available</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">400</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) > 1 & pkgbuild::has_compiler()) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">401</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">402</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Translate the R code for the derivatives to C code</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">403</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- paste(diffs, collapse = ";\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">404</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- paste0(diffs.C, ";")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">405</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">406</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # HS</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">407</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">408</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">409</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in seq_along(diffs)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">410</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state_var <- names(diffs)[i]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">411</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">412</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # IORE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">413</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (state_var %in% obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">414</td> + <td class="coverage">8343<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (spec[[state_var]]$type == "IORE") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">415</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- gsub(paste0(state_var, "^N_", state_var),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">416</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> paste0("pow(y[", i - 1, "], N_", state_var, ")"),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">417</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C, fixed = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">418</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">419</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">420</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">421</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Replace d_... terms by f[i-1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">422</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # First line</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">423</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pattern <- paste0("^d_", state_var)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">424</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> replacement <- paste0("\nf[", i - 1, "]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">425</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- gsub(pattern, replacement, diffs.C)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">426</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Other lines</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">427</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pattern <- paste0("\\nd_", state_var)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">428</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> replacement <- paste0("\nf[", i - 1, "]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">429</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- gsub(pattern, replacement, diffs.C)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">430</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">431</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Replace names of observed variables by y[i],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">432</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # making the implicit assumption that the observed variables only occur after "* "</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">433</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pattern <- paste0("\\* ", state_var)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">434</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> replacement <- paste0("* y[", i - 1, "]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">435</td> + <td class="coverage">8347<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C <- gsub(pattern, replacement, diffs.C)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">436</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">437</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">438</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">439</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f = "numeric", rpar = "numeric", ipar = "integer")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">440</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">441</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Declare the time variable in the body of the function if it is used</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">442</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">443</td> + <td class="coverage">1060<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste0("double time = *t;\n", diffs.C)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">444</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">445</td> + <td class="coverage">2668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs.C</pre> + </td> + </tr> + <tr class="never"> + <td class="num">446</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">447</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">448</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define the function initializing the parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">449</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> npar <- length(parms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">450</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> initpar_code <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">451</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "static double parms [", npar, "];\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">452</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">453</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">454</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "void initpar(void (* odeparms)(int *, double *)) {\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">455</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> " int N = ", npar, ";\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">456</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> " odeparms(&N, parms);\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">457</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "}\n\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">458</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">459</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Try to build a shared library</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">460</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model$cf <- try(inline::cfunction(derivs_sig, derivs_code,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">461</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> otherdefs = initpar_code,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">462</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> verbose = verbose, name = "diffs",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">463</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> convention = ".C", language = "C"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">464</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> silent = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">465</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">466</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(model$cf, "try-error")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">467</td> + <td class="coverage">495<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Temporary DLL for differentials generated and loaded")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">468</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(dll_dir)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">469</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We suppress warnings, as we get a warning about a path "(embedding)" </pre> + </td> + </tr> + <tr class="never"> + <td class="num">470</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # under Windows, at least when using RStudio</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">471</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> suppressWarnings(inline::moveDLL(model$cf, name, dll_dir,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">472</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> unload = unload, overwrite = overwrite, verbose = !quiet))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">473</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">474</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model$dll_info <- inline::getDynLib(model$cf)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">475</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">476</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">477</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # }}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">478</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">479</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Attach a degradation function if an analytical solution is available</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">480</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model$deg_func <- create_deg_func(spec, use_of_ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">481</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">482</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(model) <- "mkinmod"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">483</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(model)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">484</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">485</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">486</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print mkinmod objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">487</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">488</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print mkinmod objects in a way that the user finds his way to get to its</pre> + </td> + </tr> + <tr class="never"> + <td class="num">489</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' components.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">490</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">491</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">492</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An \code{\link{mkinmod}} object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">493</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">494</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mkinmod <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">495</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<mkinmod> model generated with\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">496</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Use of formation fractions $use_of_ff:", x$use_of_ff, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">497</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Specification $spec:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">498</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs in names(x$spec)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">499</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("$", obs, "\n", sep = "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">500</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spl <- x$spec[[obs]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">501</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("$type:", spl$type)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">502</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(spl$to) && length(spl$to)) cat("; $to: ", paste(spl$to, collapse = ", "), sep = "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">503</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("; $sink: ", spl$sink, sep = "")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">504</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(spl$full_name)) if (!is.na(spl$full_name)) cat("; $full_name:", spl$full_name)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">505</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">506</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">507</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.matrix(x$coefmat)) cat("Coefficient matrix $coefmat available\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">508</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$cf)) cat("Compiled model $cf available\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">509</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Differential equations:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">510</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">511</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">512</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">513</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># vim: set foldmethod=marker ts=2 sw=2 expandtab:</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mhmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Fit nonlinear mixed-effects models built from one or more kinetic</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation models and one or more error models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The name of the methods expresses that (**m**ultiple) **h**ierarchichal</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (also known as multilevel) **m**ulticompartment **kin**etic models are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitted. Our kinetic models are nonlinear, so we can use various nonlinear</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mixed-effects model fitting functions.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param objects A list of [mmkin] objects containing fits of the same</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation models to the same data, but using different error models.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Alternatively, a single [mmkin] object containing fits of several</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation models to the same data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param backend The backend to be used for fitting. Currently, only saemix is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' supported</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param no_random_effect Default is NULL and will be passed to [saem]. If a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' character vector is supplied, it will be passed to all calls to [saem],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' which will exclude random effects for all matching parameters. Alternatively,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a list of character vectors or an object of class [illparms.mhmkin] can be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' specified. They have to have the same dimensions that the return object of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the current call will have, i.e. the number of rows must match the number</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of degradation models in the mmkin object(s), and the number of columns must</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' match the number of error models used in the mmkin object(s).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param algorithm The algorithm to be used for fitting (currently not used)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments that will be passed to the nonlinear mixed-effects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model fitting function.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cores The number of cores to be used for multicore processing. This</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is only used when the \code{cluster} argument is \code{NULL}. On Windows</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' machines, cores > 1 is not supported, you need to use the \code{cluster}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' argument to use multiple logical processors. Per default, all cores detected</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' by [parallel::detectCores()] are used, except on Windows where the default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is 1.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cluster A cluster as returned by [makeCluster] to be used for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parallel execution.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom parallel mclapply parLapply detectCores</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A two-dimensional [array] of fit objects and/or try-errors that can</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be indexed using the degradation model names for the first index (row index)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and the error model names for the second index (column index), with class</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' attribute 'mhmkin'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso \code{\link{[.mhmkin}} for subsetting [mhmkin] objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mhmkin <- function(objects, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("mhmkin")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mhmkin.mmkin <- function(objects, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">49</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> mhmkin(list(objects), ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We start with separate evaluations of all the first six datasets with two</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # degradation models and two error models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_sep_const <- mmkin(c("SFO", "FOMC"), ds_fomc[1:6], cores = 2, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_sep_tc <- update(f_sep_const, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The mhmkin function sets up hierarchical degradation models aka</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # nonlinear mixed-effects models for all four combinations, specifying</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # uncorrelated random effects for all degradation parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_1 <- mhmkin(list(f_sep_const, f_sep_tc), cores = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' status(f_saem_1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The 'illparms' function shows that in all hierarchical fits, at least</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # one random effect is ill-defined (the confidence interval for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # random effect expressed as standard deviation includes zero)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Therefore we repeat the fits, excluding the ill-defined random effects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_2 <- update(f_saem_1, no_random_effect = illparms(f_saem_1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' status(f_saem_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Model comparisons show that FOMC with two-component error is preferable,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # and confirms our reduction of the default parameter model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The convergence plot for the selected model looks fine</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' saemix::plot(f_saem_2[["FOMC", "tc"]]$so, plot.type = "convergence")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The plot of predictions versus data shows that we have a pretty data-rich</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # situation with homogeneous distribution of residuals, because we used the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # same degradation model, error model and parameter distribution model that</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # was used in the data generation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem_2[["FOMC", "tc"]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can specify the same parameter model reductions manually</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' no_ranef <- list("parent_0", "log_beta", "parent_0", c("parent_0", "log_beta"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dim(no_ranef) <- c(2, 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_2m <- update(f_saem_1, no_random_effect = no_ranef)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_2m)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mhmkin.list <- function(objects, backend = "saemix", algorithm = "saem",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> no_random_effect = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- match.call()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dot_args <- list(...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> backend_function <- switch(backend,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saemix = "saem"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deg_models <- lapply(objects[[1]][, 1], function(x) x$mkinmod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(deg_models) <- dimnames(objects[[1]])$model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.deg <- length(deg_models)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds <- lapply(objects[[1]][1, ], function(x) x$data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (other in objects[-1]) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check if the degradation models in all objects are the same</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (deg_model_name in names(deg_models)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">750<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all.equal(other[[deg_model_name, 1]]$mkinmod$spec,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">750<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deg_models[[deg_model_name]]$spec))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">113</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The mmkin objects have to be based on the same degradation models")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check if they have been fitted to the same dataset</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> other_object_ds <- lapply(other[1, ], function(x) x$data)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:length(ds)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">2250<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all.equal(ds[[i]][c("time", "variable", "observed")],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">2250<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> other_object_ds[[i]][c("time", "variable", "observed")]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">122</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The mmkin objects have to be fitted to the same datasets")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.o <- length(objects)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_models = sapply(objects, function(x) x[[1]]$err_mod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.e <- length(error_models)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.fits <- n.deg * n.e</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_indices <- matrix(1:n.fits, ncol = n.e)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(fit_indices) <- list(degradation = names(deg_models),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error = error_models)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(no_random_effect) || is.null(dim(no_random_effect))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_ranef <- rep(list(no_random_effect), n.fits)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(no_ranef) <- dim(fit_indices)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(dim(no_random_effect), dim(fit_indices))) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">142</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Dimensions of argument 'no_random_effect' are not suitable")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is(no_random_effect, "illparms.mhmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_ranef_dim <- dim(no_random_effect)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_ranef <- lapply(no_random_effect, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_ranef_split <- strsplit(x, ", ")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret <- sapply(no_ranef_split, function(y) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> gsub("sd\\((.*)\\)", "\\1", y)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ret)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(no_ranef) <- no_ranef_dim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">121<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> no_ranef <- no_random_effect</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_function <- function(fit_index) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> w <- which(fit_indices == fit_index, arr.ind = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deg_index <- w[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_index <- w[2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mmkin_row <- objects[[error_index]][deg_index, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- try(do.call(backend_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">165</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> args = c(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> list(mmkin_row),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dot_args,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> list(no_random_effect = no_ranef[[deg_index, error_index]]))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">12<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_time <- system.time({</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(cluster)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> results <- parallel::mclapply(as.list(1:n.fits), fit_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mc.cores = cores, mc.preschedule = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">178</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attributes(results) <- attributes(fit_indices)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(results, "call") <- call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(results, "time") <- fit_time</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">185</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(results) <- switch(backend,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saemix = c("mhmkin.saem.mmkin", "mhmkin")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">363<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(results)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Subsetting method for mhmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">192</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An [mhmkin] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param i Row index selecting the fits for specific models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">195</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param j Column index selecting the fits to specific datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param drop If FALSE, the method always returns an mhmkin object, otherwise</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' either a list of fit objects or a single fit object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object inheriting from \code{\link{mhmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">`[.mhmkin` <- function(x, i, j, ..., drop = FALSE) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">202</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> original_class <- class(x)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">203</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">204</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> x_sub <- x[i, j, drop = drop]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">205</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">206</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!drop) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">207</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> class(x_sub) <- original_class</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">209</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(x_sub)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print method for mhmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mhmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<mhmkin> object\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Status of individual fits:\n\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(status(x))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">222</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Check if fit within an mhmkin object failed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">223</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x The object to be checked</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">check_failed <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">1936<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(x, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">226</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">1936<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(x$so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">229</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">1936<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">235</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">237</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">AIC.mhmkin <- function(object, ..., k = 2) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">238</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- sapply(object, function(x) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">239</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (check_failed(x)) return(NA)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(AIC(x$so, k = k))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(res) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(res) <- dimnames(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">244</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">245</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">247</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">248</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">BIC.mhmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- sapply(object, function(x) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">250</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (check_failed(x)) return(NA)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">500<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(BIC(x$so))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">252</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(res) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">254</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(res) <- dimnames(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">255</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.mhmkin <- function(object, ..., evaluate = TRUE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">260</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- attr(object, "call")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">261</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # For some reason we get mhkin.list in call[[1]] when using mhmkin from the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # loaded package so we need to fix this so we do not have to export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">263</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # mhmkin.list in addition to the S3 method mhmkin</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[1]] <- mhmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments <- match.call(expand.dots = FALSE)$...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">267</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(update_arguments) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_in_call <- !is.na(match(names(update_arguments), names(call)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">270</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (a in names(update_arguments)[update_arguments_in_call]) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">273</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call[[a]] <- update_arguments[[a]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">274</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">275</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">276</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_not_in_call <- !update_arguments_in_call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">277</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(any(update_arguments_not_in_call)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- c(as.list(call), update_arguments[update_arguments_not_in_call])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- as.call(call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">280</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(evaluate) eval(call, parent.frame())</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">282</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">283</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">284</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">285</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">286</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">anova.mhmkin <- function(object, ...,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">287</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method = c("is", "lin", "gq"), test = FALSE, model.names = "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">288</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(model.names, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">289</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model.names <- outer(rownames(object), colnames(object), paste)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">290</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">291</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> failed_index <- which(sapply(object, check_failed), arr.ind = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">292</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(failed_index > 0)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">293</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> rlang::inject(anova(!!!(object[-failed_index]), method = method, test = test,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">294</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model.names = model.names[-failed_index]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">295</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">296</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rlang::inject(anova(!!!(object), method = method, test = test,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">297</td> + <td class="coverage">234<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model.names = model.names))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">299</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">300</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/nafta.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Evaluate parent kinetics using the NAFTA guidance</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and returns an object of class \code{nafta} that has methods for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and plotting.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ds A dataframe that must contain one variable called "time" with the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time values specified by the \code{time} argument, one column called</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "name" with the grouping of the observed values, and finally one column of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed values called "value".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param title Optional title of the dataset</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param quiet Should the evaluation text be shown?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments passed to \code{\link{mmkin}} (not for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' printing method).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats qf</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An list of class \code{nafta}. The list element named "mmkin" is the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mmkin}} object containing the fits of the three models. The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list element named "title" contains the title of the dataset used. The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list element "data" contains the dataset used in the fits.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @source NAFTA (2011) Guidance for evaluating and calculating degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetics in environmental media. NAFTA Technical Working Group on</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Pesticides</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' accessed 2019-02-22</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculate Representative Half-life Values and Characterizing Pesticide</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(nafta_evaluation)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(nafta_evaluation)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nafta <- function(ds, title = NA, quiet = FALSE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">264<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(levels(ds$name)) > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The NAFTA procedure is only defined for decline data for a single compound")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n <- nrow(subset(ds, !is.na(value)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> models <- c("SFO", "IORE", "DFOP")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- list(title = title, data = ds)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$mmkin <- mmkin(models, list(ds), quiet = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> distimes <- lapply(result$mmkin, function(x) as.numeric(endpoints(x)$distimes["parent", ]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$distimes <- matrix(NA, nrow = 3, ncol = 3,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(models, c("DT50", "DT90", "DT50_rep")))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$distimes["SFO", ] <- distimes[[1]][c(1, 2, 1)]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$distimes["IORE", ] <- distimes[[2]][c(1, 2, 3)]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$distimes["DFOP", ] <- distimes[[3]][c(1, 2, 5)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get parameters with statistics</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$parameters <- lapply(result$mmkin, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">528<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> summary(x)$bpar[, c(1, 4:6)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(result$parameters) <- models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Compare the sum of squared residuals (SSR) to the upper bound of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # confidence region of the SSR for the IORE model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$S <- sapply(result$mmkin, function(x) sum(x$data$residual^2))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(result$S) <- c("SFO", "IORE", "DFOP")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Equation (3) on p. 3</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> p <- 3</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$S["IORE"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$S_c <- result$S[["IORE"]] * (1 + p/(n - p) * qf(0.5, p, n - p))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$t_rep <- .evaluate_nafta_results(result$S, result$S_c,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result$distimes, quiet = quiet)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "nafta"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot the results of the three models used in the NAFTA scheme.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The plots are ordered with increasing complexity of the model in this</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function (SFO, then IORE, then DFOP).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calls \code{\link{plot.mmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An object of class \code{\link{nafta}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param legend Should a legend be added?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param main Possibility to override the main title of the plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments passed to \code{\link{plot.mmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot.nafta <- function(x, legend = FALSE, main = "auto", ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (main == "auto") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">94</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.na(x$title)) main = ""</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else main = x$title</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(x$mmkin, ..., legend = legend, main = main)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print nafta objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print nafta objects. The results for the three models are printed in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An \code{\link{nafta}} object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to be used for printing parameters and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dissipation times.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname nafta</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.nafta <- function(x, quiet = TRUE, digits = 3, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Sums of squares:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$S)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nCritical sum of squares for checking the SFO model:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$S_c)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nParameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$parameters, digits = digits)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nDTx values:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(signif(x$distimes, digits = digits))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nRepresentative half-life:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(round(t_rep, 2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">.evaluate_nafta_results <- function(S, S_c, distimes, quiet = FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_SFO <- distimes["IORE", "DT50"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_IORE <- distimes["IORE", "DT50_rep"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_DFOP2 <- distimes["DFOP", "DT50_rep"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (S["SFO"] < S_c) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">130</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">131</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("S_SFO is lower than the critical value S_c, use the SFO model")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">133</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> t_rep <- t_SFO</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> message("The SFO model is rejected as S_SFO is equal or higher than the critical value S_c")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (t_IORE < t_DFOP2) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> message("The half-life obtained from the IORE model may be used")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_rep <- t_IORE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">145</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("The representative half-life of the IORE model is longer than the one corresponding")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">146</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("to the terminal degradation rate found with the DFOP model.")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">147</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("The representative half-life obtained from the DFOP model may be used")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_rep <- t_DFOP2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(t_rep)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/summary.nlme.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Summary method for class "nlme.mmkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Lists model equations, initial parameter values, optimised parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for fixed effects (population), random effects (deviations from the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' population mean) and residual error model, as well as the resulting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints such as formation fractions and DT50 values. Optionally</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (default is FALSE), the data are listed in full.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object an object of class [nlme.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x an object of class [summary.nlme.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data logical, indicating whether the full data should be included in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose Should the summary be verbose?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param distimes logical, indicating whether DT50 and DT90 values should be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' included.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha error level for confidence interval estimation from the t</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' distribution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots optional arguments passed to methods like \code{print}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The summary function returns a list based on the [nlme] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' obtained in the fit, with at least the following additional components</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{nlmeversion, mkinversion, Rversion}{The nlme, mkin and R versions used}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{date.fit, date.summary}{The dates where the fit and the summary were</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' produced}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{diffs}{The differential equations used in the degradation model}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{use_of_ff}{Was maximum or minimum use made of formation fractions}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{data}{The data}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{confint_back}{Backtransformed parameters, with confidence intervals if available}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{ff}{The estimated formation fractions derived from the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{distimes}{The DT50 and DT90 values for each observed variable.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The print method is called for its side effect, i.e. printing the summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats predict</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke for the mkin specific parts</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' José Pinheiro and Douglas Bates for the components inherited from nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Generate five datasets following SFO kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dt50_sfo_in_pop <- 50</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k_in_pop <- log(2) / dt50_sfo_in_pop</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(1234)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k_in <- rlnorm(5, log(k_in_pop), 0.5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO <- mkinmod(parent = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' pred_sfo <- function(k) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = k),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_sfo_mean <- lapply(k_in, pred_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(ds_sfo_mean) <- paste("ds", 1:5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(12345)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' add_err(ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n = 1)[[1]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Evaluate using mmkin and nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme <- nlme(f_mmkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(f_nlme, data = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(object$mkinmod$diffs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_trans <- intervals(object, which = "fixed", level = 1 - alpha)$fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(confint_trans, "label") <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pnames <- rownames(confint_trans)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates, object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpnames <- names(bp)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # variance-covariance estimates for fixed effects (from summary.lme)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed <- fixef(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stdFixed <- sqrt(diag(as.matrix(object$varFix)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$corFixed <- array(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t(object$varFix/stdFixed)/stdFixed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(object$varFix),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> list(names(fixed), names(fixed)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform boundaries of CI for one parameter at a time,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # with the exception of sets of formation fractions (single fractions are OK).</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names_skip <- character(0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) { # Figure out sets of fractions to skip</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">436<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">436<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_paths <- length(f_names)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">100</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back <- matrix(NA, nrow = length(bp), ncol = 3,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(bpnames, colnames(confint_trans)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[, "est."] <- bp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in pnames) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!pname %in% f_names_skip) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.lower <- confint_trans[pname, "lower"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.upper <- confint_trans[pname, "upper"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(par.lower) <- names(par.upper) <- pname</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpl <- backtransform_odeparms(par.lower, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpu <- backtransform_odeparms(par.upper, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpl), "lower"] <- bpl</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">1410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpu), "upper"] <- bpu</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_trans <- confint_trans</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_back <- confint_back</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$date.summary = date()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$use_of_ff = object$mkinmod$use_of_ff</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$error_model_algorithm = object$mmkin[[1]]$error_model_algorithm</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod = object$mmkin[[1]]$err_mod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$diffs <- object$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$print_data <- data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["observed"]] <- object$data[["value"]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["value"]] <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["predicted"]] <- predict(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["residual"]] <- residuals(object, type = "response")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(object$modelStruct$varStruct)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">138</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["std"]] <- object$sigma</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["std"]] <- 1/attr(object$modelStruct$varStruct, "weights")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[["standardized"]] <- residuals(object, type = "pearson")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$verbose <- verbose</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$fixed <- object$mmkin[[1]]$fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$AIC = AIC(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$BIC = BIC(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$logLik = logLik(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep <- endpoints(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$ff) != 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$ff <- ep$ff</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (distimes) object$distimes <- ep$distimes</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">154</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(object) <- c("summary.nlme.mmkin", "nlme.mmkin", "nlme", "lme")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">319<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary.nlme.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.summary.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("nlme version used for fitting: ", x$nlmeversion, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("mkin version used for pre-fitting: ", x$mkinversion, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("R version used for fitting: ", x$Rversion, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of fit: ", x$date.fit, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of summary:", x$date.summary, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEquations:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(nrow(x$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$ds)), "datasets\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nModel predictions using solution type", x$solution_type, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFitted in", x$time[["elapsed"]], "s using", x$numIter, "iterations\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nVariance model: ")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(switch(x$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "Constant variance",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">185</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = "Variance unique to each observed variable",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = "Two-component variance function"), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nMean of starting values for individual parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$mean_dp_start, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFixed degradation parameter values:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(x$fixed$value) == 0) cat("None\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">193</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else print(x$fixed, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResults:\n\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = " "), digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_trans, digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(x$confint_trans) > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">203</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> corr <- x$corFixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(corr) <- "correlation"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(corr, title = "\nCorrelation:", rdig = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n") # Random effects</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(summary(x$modelStruct), sigma = x$sigma,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> reEstimates = x$coef$random, digits = digits, verbose = verbose, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nBacktransformed parameters with asymmetric confidence intervals:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_back, digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printSFORB <- !is.null(x$SFORB)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printSFORB){</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">218</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated Eigenvalues of SFORB model(s):\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">219</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$SFORB, digits = digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printff <- !is.null(x$ff)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printff){</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">224</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResulting formation fractions:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">225</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(ff = x$ff), digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printdistimes <- !is.null(x$distimes)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printdistimes){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated disappearance times:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$distimes, digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (x$print_data){</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">235</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">236</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(format(x$data, digits = digits, ...), row.names = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">237</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">240</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinerrplot.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("variable", "residual"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to plot squared residuals and the error model for an mkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function plots the squared residuals for the specified subset of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed variables from an mkinfit object. In addition, one or more dashed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' line(s) show the fitted error model. A combined plot of the fitted model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and this error model plot can be obtained with \code{\link{plot.mkinfit}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' using the argument \code{show_errplot = TRUE}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A fit represented in an \code{\link{mkinfit}} object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param obs_vars A character vector of names of the observed variables for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' which residuals should be plotted. Defaults to all observed variables in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlim plot range in x direction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlab Label for the x axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ylab Label for the y axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param maxy Maximum value of the residuals. This is used for the scaling of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the y axis and defaults to "auto".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param legend Should a legend be plotted?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lpos Where should the legend be placed? Default is "topright". Will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be passed on to \code{\link{legend}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param col_obs Colors for the observed variables.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pch_obs Symbols to be used for the observed variables.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param frame Should a frame be drawn around the plots?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots further arguments passed to \code{\link{plot}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Nothing is returned by this function, as it is called for its side</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' effect, namely to produce a plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso \code{\link{mkinplot}}, for a way to plot the data and the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lines of the mkinfit object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @keywords hplot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(model, FOCUS_2006_D, error_model = "tc", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinerrplot(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinerrplot <- function (object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars = names(object$mkinmod$map),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = c(0, 1.1 * max(object$data$predicted)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "Predicted", ylab = "Squared residual",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> maxy = "auto", legend= TRUE, lpos = "topright",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> col_obs = "auto", pch_obs = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> frame = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars_all <- as.character(unique(object$data$variable))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) > 0){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- intersect(obs_vars_all, obs_vars)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">55</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> } else obs_vars <- obs_vars_all</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals <- subset(object$data, variable %in% obs_vars, residual)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (maxy == "auto") maxy = max(residuals^2, na.rm = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set colors and symbols</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (col_obs[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col_obs <- 1:length(obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pch_obs[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_obs <- 1:length(obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(col_obs) <- names(pch_obs) <- obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = xlab, ylab = ylab,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = xlim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = c(0, 1.2 * maxy), frame = frame, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for(obs_var in obs_vars){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals_plot <- subset(object$data, variable == obs_var, c("predicted", "residual"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(residuals_plot[["predicted"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals_plot[["residual"]]^2,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch = pch_obs[obs_var], col = col_obs[obs_var])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "const") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = object$errparms^2, lty = 2, col = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "obs") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">130<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_name = paste0("sigma_", obs_var)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">130<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = object$errparms[sigma_name]^2, lty = 2,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">130<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_obs[obs_var])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_plot <- function(predicted) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_twocomp(predicted,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_low = object$errparms[1],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rsd_high = object$errparms[2])^2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(sigma_plot, from = 0, to = max(object$data$predicted),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add = TRUE, lty = 2, col = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">275<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (legend == TRUE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend(lpos, inset = c(0.05, 0.05), legend = obs_vars,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_obs[obs_vars], pch = pch_obs[obs_vars])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/parplot.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot parameter variability of multistart objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Produces a boxplot with all parameters from the multiple runs, scaled</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' either by the parameters of the run with the highest likelihood,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' or by their medians as proposed in the paper by Duchesne et al. (2021).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Starting values of degradation model parameters and error model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are shown as green circles. The results obtained in the original run</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are shown as red circles.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The [multistart] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param llmin The minimum likelihood of objects to be shown</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param llquant Fractional value for selecting only the fits with higher</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' likelihoods. Overrides 'llmin'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param scale By default, scale parameters using the best</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' available fit.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If 'median', parameters are scaled using the median parameters from all fits.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param main Title of the plot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lpos Positioning of the legend.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Passed to [boxplot]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' identifiability in the frame of nonlinear mixed effects models: the example</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' doi: 10.1186/s12859-021-04373-4.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [multistart]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats median quantile</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parplot <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("parplot")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname parplot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> scale = c("best", "median"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> lpos = "bottomleft", main = "", ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig <- attr(object, "orig")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig_parms <- parms(orig)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_degparms <- orig$mean_dp_start</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_parms <- parms(object, exclude_failed = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object, "multistart.saem.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llfunc <- function(object) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">48</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object$so, "try-error")) return(NA)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">1408<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(logLik(object$so))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">52</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("parplot is only implemented for multistart.saem.mmkin objects")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll <- sapply(object, llfunc)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(llquant[1])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">56</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (llmin != -Inf) warning("Overriding 'llmin' because 'llquant' was specified")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llmin <- quantile(ll, 1 - llquant)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> selected <- which(ll > llmin)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> selected_parms <- all_parms[selected, ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(las = 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (orig$transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_names_transformed <- names(start_degparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_index <- which(names(orig_parms) %in% degparm_names_transformed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig_parms[degparm_names_transformed] <- backtransform_odeparms(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig_parms[degparm_names_transformed],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig$mmkin[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = orig$mmkin[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = orig$mmkin[[1]]$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_degparms <- backtransform_odeparms(start_degparms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig$mmkin[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = orig$mmkin[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = orig$mmkin[[1]]$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_names <- names(start_degparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(orig_parms) <- c(degparm_names, names(orig_parms[-degparm_index]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> selected_parms[, degparm_names_transformed] <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t(apply(selected_parms[, degparm_names_transformed], 1, backtransform_odeparms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig$mmkin[[1]]$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = orig$mmkin[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = orig$mmkin[[1]]$transform_fractions))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(selected_parms)[1:length(degparm_names)] <- degparm_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_errparms <- orig$so@model@error.init</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(start_errparms) <- orig$so@model@name.sigma</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_omegaparms <- orig$so@model@omega.init</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_parms <- c(start_degparms, start_errparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> scale <- match.arg(scale)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_scale <- switch(scale,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> best = selected_parms[which.best(object[selected]), ],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> median = apply(selected_parms, 2, median)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Boxplots of all scaled parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> selected_scaled_parms <- t(apply(selected_parms, 1, function(x) x / parm_scale))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> boxplot(selected_scaled_parms, log = "y", main = main, ,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylab = "Normalised parameters", ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show starting parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_scaled_parms <- rep(NA_real_, length(orig_parms))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(start_scaled_parms) <- names(orig_parms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_scaled_parms[names(start_parms)] <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_parms / parm_scale[names(start_parms)]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(start_scaled_parms, col = 3, cex = 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show parameters of original run</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> orig_scaled_parms <- orig_parms / parm_scale</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(orig_scaled_parms, col = 2, cex = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = 1, lty = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend(lpos, inset = c(0.05, 0.05), bty = "n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch = 1, col = 3:1, lty = c(NA, NA, 1),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend = c(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Original start",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Original results",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Multistart runs"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/plot.mixed.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables("ds")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An object of class [mixed.mmkin], [saem.mmkin] or [nlme.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param i A numeric index to select datasets for which to plot the individual predictions,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in case plots get too large</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inheritParams plot.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param standardized Should the residuals be standardized? Only takes effect if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' `resplot = "time"`.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pop_curves Per default, one population curve is drawn in case</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' population parameters are fitted by the model, e.g. for saem objects.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' In case there is a covariate model, the behaviour depends on the value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of 'covariates'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariates Data frame with covariate values for all variables in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' any covariate models in the object. If given, it overrides 'covariate_quantiles'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Each line in the data frame will result in a line drawn for the population.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Rownames are used in the legend to label the lines.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param covariate_quantiles This argument only has an effect if the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' object has covariate models. If so, the default is to show three population</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' curves, for the 5th percentile, the 50th percentile and the 95th percentile</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the covariate values used for fitting the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note Covariate models are currently only supported for saem.mmkin objects.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pred_over Named list of alternative predictions as obtained</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from [mkinpredict] with a compatible [mkinmod].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param test_log_parms Passed to [mean_degparms] in the case of an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mixed.mmkin] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param conf.level Passed to [mean_degparms] in the case of an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mixed.mmkin] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param default_log_parms Passed to [mean_degparms] in the case of an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mixed.mmkin] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rel.height.legend The relative height of the legend shown on top</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rel.height.bottom The relative height of the bottom plot row</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ymax Vector of maximum y axis values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ncol.legend Number of columns to use in the legend</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param nrow.legend Number of rows to use in the legend</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param resplot Should the residuals plotted against time or against</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' predicted values?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param col_ds Colors used for plotting the observed data and the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' corresponding model prediction lines for the different datasets.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pch_ds Symbols to be used for plotting the data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lty_ds Line types to be used for the model predictions.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats coefficients</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds <- lapply(experimental_data_for_UBA_2019[6:10],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(x) x$data[c("name", "time", "value")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(ds) <- paste0("ds ", 6:10)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f[, 3:4], standardized = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # For this fit we need to increase pnlsMaxiter, and we increase the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # tolerance in order to speed up the fit for this example evaluation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # It still takes 20 seconds to run</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem <- saem(f, transformations = "saemix")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_obs <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, error_model = "obs")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlmix <- nlmix(f_obs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlmix)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can overlay the two variants if we generate predictions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' pred_nlme <- mkinpredict(dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme$bparms.optim[-1],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = f_nlme$bparms.optim[[1]], A1 = 0),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' seq(0, 180, by = 0.2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_saem, pred_over = list(nlme = pred_nlme))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot.mixed.mmkin <- function(x,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> i = 1:ncol(x$mmkin),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars = names(x$mkinmod$map),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_quantiles = c(0.5, 0.05, 0.95),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "Time",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = range(x$data$time),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> resplot = c("predicted", "time"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_over = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> test_log_parms = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.level = 0.6,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> default_log_parms = NA,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ymax = "auto", maxabs = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> nrow.legend = ceiling((length(i) + 1) / ncol.legend),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> rel.height.legend = 0.02 + 0.07 * nrow.legend,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> rel.height.bottom = 1.1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_ds = 1:length(i),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> col_ds = pch_ds + 1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> lty_ds = col_ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> frame = TRUE, ...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Prepare parameters and data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_1 <- x$mmkin[[1]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_names <- colnames(x$mmkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> backtransform = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(class(x), "mixed.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(pop_curves, "auto")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">110</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pop_curves) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_pop <- mean_degparms(x$mmkin, test_log_parms = test_log_parms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.level = conf.level, default_log_parms = default_log_parms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_tmp <- parms(x$mmkin, transformed = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_i <- as.data.frame(t(degparms_tmp[setdiff(rownames(degparms_tmp), names(fit_1$errparms)), ]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residual_type = ifelse(standardized, "standardized", "residual")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals <- x$data[[residual_type]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(x, "nlme.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(pop_curves, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">129</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_i <- coefficients(x)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_pop <- nlme::fixef(x)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals <- residuals(x,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> type = ifelse(standardized, "pearson", "response"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(x, "saem.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (x$transformations == "saemix") backtransform = FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> psi <- saemix::psi(x$so)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(psi) <- x$saemix_ds_order</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_i <- psi[ds_names, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_i_names <- colnames(degparms_i)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residual_type = ifelse(standardized, "standardized", "residual")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals <- x$data[[residual_type]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(pop_curves, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(x$covariate_models) == 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_pop <- x$so@results@fixed.effects</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(degparms_pop) <- degparms_i_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">152</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(covariates)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">153</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = as.data.frame(</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">154</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> apply(x$covariates, 2, quantile,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">155</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> covariate_quantiles, simplify = FALSE))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">156</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covariates) <- paste(</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">157</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(length(x$covariate_models) == 1,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">158</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "Covariate", "Covariates"),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">159</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covariates))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">161</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_pop <- parms(x, covariates = covariates)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">162</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">165</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pop_curves <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pop_curves) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Make sure degparms_pop is a matrix, columns corresponding to population curve(s)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(dim(degparms_pop))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_pop <- matrix(degparms_pop, ncol = 1,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(names(degparms_pop), "Population"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_fixed <- fit_1$fixed$value</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(degparms_fixed) <- rownames(fit_1$fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_all <- cbind(as.matrix(degparms_i),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> matrix(rep(degparms_fixed, nrow(degparms_i)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ncol = length(degparms_fixed),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nrow = nrow(degparms_i), byrow = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_all_names <- c(names(degparms_i), names(degparms_fixed))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(degparms_all) <- degparms_all_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_names <- grep("_0$", degparms_all_names, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_names <- setdiff(degparms_all_names, odeini_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- cbind(x$data[c("ds", "name", "time", "value")],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residual = residuals)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = fit_1$solution_type</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes <- sort(unique(c(x$data$time,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> seq(xlim[1], xlim[2], length.out = 50))))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_list <- lapply(i, function(ds_i) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_trans <- degparms_all[ds_i, odeparms_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeparms_trans) <- odeparms_names # needed if only one odeparm</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (backtransform) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">2620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- backtransform_odeparms(odeparms_trans,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">2620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">203</td> + <td class="coverage">2620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = fit_1$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">2620<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = fit_1$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">205</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">325<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- odeparms_trans</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- degparms_all[ds_i, odeini_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini) <- gsub("_0", "", odeini_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- mkinpredict(x$mkinmod, odeparms, odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes, solution_type = solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">2945<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = fit_1$atol, rtol = fit_1$rtol)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(pred_list) <- ds_names[i]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_ds <- vctrs::vec_rbind(!!!pred_list, .names_to = "ds")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pop_curves) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">220</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_list_pop <- lapply(1:ncol(degparms_pop), function(cov_i) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_all_pop_i <- c(degparms_pop[, cov_i], degparms_fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_pop_trans_i <- degparms_all_pop_i[odeparms_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeparms_pop_trans_i) <- odeparms_names # needed if only one odeparm</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (backtransform) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_pop_i <- backtransform_odeparms(odeparms_pop_trans_i,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">226</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">227</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = fit_1$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = fit_1$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">229</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_pop_i <- odeparms_pop_trans_i</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- degparms_all_pop_i[odeini_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini) <- gsub("_0", "", odeini_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">235</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- mkinpredict(x$mkinmod, odeparms_pop_i, odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes, solution_type = solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">238</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = fit_1$atol, rtol = fit_1$rtol)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">239</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(pred_list_pop) <- colnames(degparms_pop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">243</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pred_list_pop <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">245</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Start of graphical section</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">249</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">250</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plot_rows = length(obs_vars)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plots = n_plot_rows * 2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">252</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">253</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set relative plot heights, so the first plot row is the norm</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">254</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rel.heights <- if (n_plot_rows > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">255</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">257</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c(rel.height.legend, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">260</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">261</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plot_rows + 1, 2, byrow = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">262</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout(layout_matrix, heights = rel.heights)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">263</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(0.1, 2.1, 0.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">266</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Empty plot with legend</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">267</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(pred_over)) lty_over <- seq(2, length.out = length(pred_over))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else lty_over <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pop_curves) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">270</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(covariates)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">271</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lty_pop <- 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(lty_pop) <- "Population"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">273</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">274</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lty_pop <- 1:nrow(covariates)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">275</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> names(lty_pop) <- rownames(covariates)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">276</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">277</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">278</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lty_pop <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">279</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_pop_over <- length(lty_pop) + length(lty_over)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">281</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">282</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n", axes = FALSE, ann = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">283</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend("center", bty = "n", ncol = ncol.legend,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend = c(names(lty_pop), names(pred_over), ds_names[i]),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lty = c(lty_pop, lty_over, lty_ds),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">286</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lwd = c(rep(2, n_pop_over), rep(1, length(i))),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">287</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = c(rep(1, n_pop_over), col_ds),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">288</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch = c(rep(NA, n_pop_over), pch_ds))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">289</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">290</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> resplot <- match.arg(resplot)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">291</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">292</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Loop plot rows</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">293</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (plot_row in 1:n_plot_rows) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">294</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">295</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_var <- obs_vars[plot_row]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">296</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed_row <- subset(observed, name == obs_var)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">297</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set ylim to sensible default, or use ymax</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">299</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(ymax, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">300</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim_row = c(0,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">301</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max(c(observed_row$value, pred_ds[[obs_var]]), na.rm = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">302</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">303</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ylim_row = c(0, ymax[plot_row])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">304</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">305</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">306</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for bottom row of plots when we have more than one row</pre> + </td> + </tr> + <tr class="never"> + <td class="num">307</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # This is the only row that needs to show the x axis legend</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">308</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (plot_row == n_plot_rows) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">309</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(5.1, 4.1, 1.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">310</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">311</td> + <td class="coverage">218<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3.0, 4.1, 1.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">312</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">313</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">314</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">315</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = xlim, ylim = ylim_row,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">316</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = xlab, ylab = paste("Residues", obs_var), frame = frame)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">317</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">318</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(pred_over)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">319</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (i_over in seq_along(pred_over)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">320</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> pred_frame <- as.data.frame(pred_over[[i_over]])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">321</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lines(pred_frame$time, pred_frame[[obs_var]],</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">322</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lwd = 2, lty = lty_over[i_over])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">323</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">324</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">325</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">326</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (ds_i in seq_along(i)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">327</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(subset(observed_row, ds == ds_names[ds_i], c("time", "value")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">328</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_ds[ds_i], pch = pch_ds[ds_i])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">329</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lines(subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">330</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_ds[ds_i], lty = lty_ds[ds_i])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">331</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">332</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">333</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pop_curves) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">334</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (cov_i in seq_along(pred_list_pop)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">335</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cov_name <- names(pred_list_pop)[cov_i]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">336</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lines(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">337</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_list_pop[[cov_i]][, "time"],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">338</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pred_list_pop[[cov_i]][, obs_var],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">339</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> type = "l", lwd = 2, lty = lty_pop[cov_i])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">340</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">341</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">342</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">343</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(maxabs, "auto")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">344</td> + <td class="coverage">283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> maxabs = max(abs(observed_row$residual), na.rm = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">345</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">346</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">347</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(resplot, "time")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">348</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n", xlim = xlim, xlab = "Time",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">349</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = c(-1.2 * maxabs, 1.2 * maxabs),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">350</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ylab = if (standardized) "Standardized residual" else "Residual",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">351</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> frame = frame)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">352</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">353</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = 0, lty = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">354</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">355</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (ds_i in seq_along(i)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">356</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> points(subset(observed_row, ds == ds_names[ds_i], c("time", "residual")),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">357</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_ds[ds_i], pch = pch_ds[ds_i])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">358</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">359</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">360</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">361</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(resplot, "predicted")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">362</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">363</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = c(0, max(pred_ds[[obs_var]])),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">364</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "Predicted",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">365</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = c(-1.2 * maxabs, 1.2 * maxabs),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">366</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylab = if (standardized) "Standardized residual" else "Residual",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">367</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> frame = frame)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">368</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">369</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = 0, lty = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">370</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">371</td> + <td class="coverage">501<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (ds_i in seq_along(i)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">372</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed_row_ds <- merge(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">373</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> subset(observed_row, ds == ds_names[ds_i], c("time", "residual")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">374</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> subset(pred_ds, ds == ds_names[ds_i], c("time", obs_var)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">375</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(observed_row_ds[c(3, 2)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">376</td> + <td class="coverage">4915<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_ds[ds_i], pch = pch_ds[ds_i])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">377</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">378</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">379</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">380</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/summary.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Summary method for class "mkinfit"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Lists model equations, initial parameter values, optimised parameters with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' some uncertainty statistics, the chi2 error levels calculated according to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS guidance (2006) as defined therein, formation fractions, DT50 values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and optionally the data, consisting of observed, predicted and residual</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' values.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object an object of class [mkinfit].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x an object of class \code{summary.mkinfit}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data logical, indicating whether the data should be included in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param distimes logical, indicating whether DT50 and DT90 values should be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' included.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha error level for confidence interval estimation from t</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' distribution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots optional arguments passed to methods like \code{print}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats qt pt cov2cor</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The summary function returns a list with components, among others</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{version, Rversion}{The mkin and R versions used}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{date.fit, date.summary}{The dates where the fit and the summary were</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' produced}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{diffs}{The differential equations used in the model}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{use_of_ff}{Was maximum or minimum use made of formation fractions}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{bpar}{Optimised and backtransformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{data}{The data (see Description above).}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{start}{The starting values and bounds, if applicable, for optimised</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{fixed}{The values of fixed parameters.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{errmin }{The chi2 error levels for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' each observed variable.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{bparms.ode}{All backtransformed ODE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters, for use as starting parameters for related models.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{errparms}{Error model parameters.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{ff}{The estimated formation fractions derived from the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{distimes}{The DT50 and DT90 values for each observed variable.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{SFORB}{If applicable, eigenvalues and fractional eigenvector component</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' g of SFORB systems in the model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The print method is called for its side effect, i.e. printing the summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(mkinfit("SFO", FOCUS_2006_A, quiet = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> param <- object$par</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pnames <- names(param)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpnames <- names(object$bparms.optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> epnames <- names(object$errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> p <- length(param)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(object$mkinmod$diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar <- try(solve(object$hessian), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar_notrans <- try(solve(object$hessian_notrans), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rdf <- object$df.residual</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.numeric(covar) | is.na(covar[1])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">66</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> covar <- NULL</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">67</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> se <- lci <- uci <- rep(NA, p)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covar) <- colnames(covar) <- pnames</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> se <- sqrt(diag(covar))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci <- param + qt(alpha/2, rdf) * se</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uci <- param + qt(1-alpha/2, rdf) * se</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> beparms.optim <- c(object$bparms.optim, object$par[epnames])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.numeric(covar_notrans) | is.na(covar_notrans[1])) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar_notrans <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> se_notrans <- tval <- pval <- rep(NA, p)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">52070<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covar_notrans) <- colnames(covar_notrans) <- c(bpnames, epnames)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">52070<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> se_notrans <- sqrt(diag(covar_notrans))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">52070<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tval <- beparms.optim / se_notrans</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">52070<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pval <- pt(abs(tval), rdf, lower.tail = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(se) <- pnames</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> param <- cbind(param, se, lci, uci)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(param) <- list(pnames, c("Estimate", "Std. Error", "Lower", "Upper"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparam <- cbind(Estimate = beparms.optim, se_notrans,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "t value" = tval, "Pr(>t)" = pval, Lower = NA, Upper = NA)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform boundaries of CI for one parameter at a time,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # with the exception of sets of formation fractions (single fractions are OK).</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names_skip <- character(0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) { # Figure out sets of fractions to skip</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">70671<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">70671<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_paths <- length(f_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">1135<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in pnames) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">293621<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!pname %in% f_names_skip) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.lower <- param[pname, "Lower"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.upper <- param[pname, "Upper"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(par.lower) <- names(par.upper) <- pname</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpl <- backtransform_odeparms(par.lower, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpu <- backtransform_odeparms(par.upper, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparam[names(bpl), "Lower"] <- bpl</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">290217<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparam[names(bpu), "Upper"] <- bpu</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparam[epnames, c("Lower", "Upper")] <- param[epnames, c("Lower", "Upper")]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans <- list(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> version = as.character(utils::packageVersion("mkin")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Rversion = paste(R.version$major, R.version$minor, sep="."),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> date.fit = object$date,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> date.summary = date(),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = object$solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warnings = object$summary_warnings,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_of_ff = object$mkinmod$use_of_ff,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model_algorithm = object$error_model_algorithm,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> df = c(p, rdf),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar = covar,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar_notrans = covar_notrans,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod = object$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> niter = object$iterations,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> calls = object$calls,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = object$time,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par = param,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpar = bparam)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(object$version)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$fit_version <- object$version</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$fit_Rversion <- object$Rversion</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ans$fit_version >= "0.9.49.6") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">52156<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$AIC = AIC(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">52156<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$BIC = BIC(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">52156<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$logLik = logLik(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$diffs <- object$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(data) ans$data <- object$data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$start <- object$start</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$start_transformed <- object$start_transformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$fixed <- object$fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$errmin <- mkinerrmin(object, alpha = 0.05)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$calls > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(ans$covar)){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Corr <- cov2cor(ans$covar)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(Corr) <- colnames(Corr) <- rownames(ans$par)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$Corr <- Corr</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">164</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Could not calculate correlation; no covariance matrix")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$bparms.ode <- object$bparms.ode</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$shapiro.p <- object$shapiro.p</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep <- endpoints(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$ff) != 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">15612<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans$ff <- ep$ff</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (distimes) ans$distimes <- ep$distimes</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">2442<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">43972<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(object$d_3_message)) ans$d_3_message <- object$d_3_message</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(ans) <- "summary.mkinfit"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">52158<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ans)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(x$fit_version)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">184</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("mkin version: ", x$version, "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">185</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("R version: ", x$Rversion, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("mkin version used for fitting: ", x$fit_version, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("R version used for fitting: ", x$fit_Rversion, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of fit: ", x$date.fit, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of summary:", x$date.summary, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEquations:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> df <- x$df</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rdf <- df[2]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nModel predictions using solution type", x$solution_type, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFitted using", x$calls, "model solutions performed in", x$time[["elapsed"]], "s\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$err_mod)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nError model: ")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(switch(x$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "Constant variance",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = "Variance unique to each observed variable",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = "Two-component variance function"), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nError model algorithm:", x$error_model_algorithm, "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">212</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">215</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStarting values for parameters to be optimised:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$start)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">217</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStarting values for the transformed parameters actually optimised:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$start_transformed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFixed parameter values:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(x$fixed$value) == 0) cat("None\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else print(x$fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We used to only have one warning - show this for summarising old objects</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">226</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x[["warning"]])) cat("\n\nWarning:", x$warning, "\n\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(x$warnings) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">229</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n\nWarning(s):", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">230</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat(x$warnings, sep = "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$AIC)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResults:\n\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = " "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">237</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nOptimised, transformed parameters with symmetric confidence intervals:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(signif(x$par, digits = digits))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (x$calls > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nParameter correlation:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">244</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$covar)){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$Corr, digits = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">247</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("No covariance matrix")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">248</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">249</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nBacktransformed parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Confidence intervals for internally transformed parameters are asymmetric.\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if ((x$version) < "0.9-36") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">254</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("To get the usual (questionable) t-test, upgrade mkin and repeat the fit.\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">255</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(signif(x$bpar, digits = digits))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">257</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("t-test (unrealistically) based on the assumption of normal distribution\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">258</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("for estimators of untransformed parameters.\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">259</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(signif(x$bpar[, c(1, 3, 4, 5, 6)], digits = digits))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">261</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">262</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFOCUS Chi2 error levels in percent:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x$errmin$err.min <- 100 * x$errmin$err.min</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$errmin, digits=digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printSFORB <- !is.null(x$SFORB)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printSFORB){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated Eigenvalues and DFOP g parameter of SFORB model(s):\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$SFORB, digits=digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">270</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printff <- !is.null(x$ff)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">273</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printff){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">274</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResulting formation fractions:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">275</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(ff = x$ff), digits=digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">276</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">277</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printdistimes <- !is.null(x$distimes)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printdistimes){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated disappearance times:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$distimes, digits=digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">282</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">283</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printdata <- !is.null(x$data)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (printdata){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">286</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">287</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(format(x$data, digits = digits, ...), row.names = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">288</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">289</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">290</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">291</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("name", "time", "value"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Fit a kinetic model to data with one or more state variables</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function maximises the likelihood of the observed data using the Port</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' algorithm [stats::nlminb()], and the specified initial or fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters and starting values. In each step of the optimisation, the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic model is solved using the function [mkinpredict()], except</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if an analytical solution is implemented, in which case the model is solved</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' using the degradation function in the [mkinmod] object. The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters of the selected error model are fitted simultaneously with the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation model parameters, as both of them are arguments of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' likelihood function.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Per default, parameters in the kinetic models are internally transformed in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' order to better satisfy the assumption of a normal distribution of their</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' estimators.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param mkinmod A list of class [mkinmod], containing the kinetic</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model to be fitted to the data, or one of the shorthand names ("SFO",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent only degradation model is generated for the variable with the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' highest value in \code{observed}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param observed A dataframe with the observed data. The first column called</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "name" must contain the name of the observed variable for each data point.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The second column must contain the times of observation, named "time".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The third column must be named "value" and contain the observed values.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Zero values in the "value" column will be removed, with a warning, in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' order to avoid problems with fitting the two-component error model. This</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is not expected to be a problem, because in general, values of zero are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' not observed in degradation data, because there is a lower limit of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' detection.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param parms.ini A named vector of initial values for the parameters,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' including parameters to be optimised and potentially also fixed parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as indicated by \code{fixed_parms}. If set to "auto", initial values for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rate constants are set to default values. Using parameter names that are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' not in the model gives an error.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' It is possible to only specify a subset of the parameters that the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' needs. You can use the parameter lists "bparms.ode" from a previously</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitted model, which contains the differential equation parameters from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' this model. This works nicely if the models are nested. An example is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' given below.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param state.ini A named vector of initial values for the state variables of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the model. In case the observed variables are represented by more than one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model variable, the names will differ from the names of the observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables (see \code{map} component of [mkinmod]). The default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is to set the initial value of the first model variable to the mean of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time zero values for the variable with the maximum observed value, and all</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' others to 0. If this variable has no time zero observations, its initial</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' value is set to 100.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param err.ini A named vector of initial values for the error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters to be optimised. If set to "auto", initial values are set to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' default values. Otherwise, inital values for all error model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' must be given.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fixed_parms The names of parameters that should not be optimised but</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rather kept at the values specified in \code{parms.ini}. Alternatively,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a named numeric vector of parameters to be fixed, regardless of the values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in parms.ini.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fixed_initials The names of model variables for which the initial</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' state at time 0 should be excluded from the optimisation. Defaults to all</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' state variables except for the first one.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param from_max_mean If this is set to TRUE, and the model has only one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed variable, then data before the time of the maximum observed value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (after averaging for each sampling time) are discarded, and this time is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' subtracted from all remaining time values, so the time of the maximum</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed mean value is the new time zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param solution_type If set to "eigen", the solution of the system of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' differential equations is based on the spectral decomposition of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' coefficient matrix in cases that this is possible. If set to "deSolve", a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' numerical [ode solver from package deSolve][deSolve::ode()] is used. If</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set to "analytical", an analytical solution of the model is used. This is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' only implemented for relatively simple degradation models. The default is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "auto", which uses "analytical" if possible, otherwise "deSolve" if a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compiler is present, and "eigen" if no compiler is present and the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' can be expressed using eigenvalues and eigenvectors.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method.ode The solution method passed via [mkinpredict()]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to [deSolve::ode()] in case the solution type is "deSolve". The default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "lsoda" is performant, but sometimes fails to converge.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param use_compiled If set to \code{FALSE}, no compiled version of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mkinmod] model is used in the calls to [mkinpredict()] even if a compiled</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' version is present.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param control A list of control arguments passed to [stats::nlminb()].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transform_rates Boolean specifying if kinetic rate constants should</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be transformed in the model specification used in the fitting for better</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compliance with the assumption of normal distribution of the estimator. If</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' TRUE, also alpha and beta parameters of the FOMC model are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' log-transformed, as well as k1 and k2 rate constants for the DFOP and HS</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' models and the break point tb of the HS model. If FALSE, zero is used as</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a lower bound for the rates in the optimisation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transform_fractions Boolean specifying if formation fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' should be transformed in the model specification used in the fitting for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' better compliance with the assumption of normal distribution of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' estimator. The default (TRUE) is to do transformations. If TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the g parameter of the DFOP model is also transformed. Transformations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' are described in [transform_odeparms].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param quiet Suppress printing out the current value of the negative</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' log-likelihood after each improvement?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param atol Absolute error tolerance, passed to [deSolve::ode()]. Default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is 1e-8, which is lower than the default in the [deSolve::lsoda()]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function which is used per default.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rtol Absolute error tolerance, passed to [deSolve::ode()]. Default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is 1e-10, much lower than in [deSolve::lsoda()].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param error_model If the error model is "const", a constant standard</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deviation is assumed.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If the error model is "obs", each observed variable is assumed to have its</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' own variance.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If the error model is "tc" (two-component error model), a two component</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' error model similar to the one described by Rocke and Lorenzato (1995) is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' used for setting up the likelihood function. Note that this model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deviates from the model by Rocke and Lorenzato, as their model implies</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' that the errors follow a lognormal distribution for large values, not a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' normal distribution as assumed by this method.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param error_model_algorithm If "auto", the selected algorithm depends on</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the error model. If the error model is "const", unweighted nonlinear</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' least squares fitting ("OLS") is selected. If the error model is "obs", or</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "tc", the "d_3" algorithm is selected.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "d_3" will directly minimize the negative log-likelihood</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and independently also use the three step algorithm described below.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The fit with the higher likelihood is returned.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "direct" will directly minimize the negative log-likelihood.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "twostep" will minimize the negative log-likelihood after an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' initial unweighted least squares optimisation step.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "threestep" starts with unweighted least squares, then</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' optimizes only the error model using the degradation model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' found, and then minimizes the negative log-likelihood with free</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation and error model parameters.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "fourstep" starts with unweighted least squares, then</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' optimizes only the error model using the degradation model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' found, then optimizes the degradation model again with fixed error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters, and finally minimizes the negative log-likelihood with free</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation and error model parameters.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' unweighted least squares, and then iterates optimization of the error</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model parameters and subsequent optimization of the degradation model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' using those error model parameters, until the error model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' converge.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param reweight.tol Tolerance for the convergence criterion calculated from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the error model parameters in IRLS fits.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param reweight.max.iter Maximum number of iterations in IRLS fits.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param trace_parms Should a trace of the parameter values be listed?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param test_residuals Should the residuals be tested for normal distribution?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments that will be passed on to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [deSolve::ode()].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats nlminb aggregate dist shapiro.test</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list with "mkinfit" in the class attribute.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note When using the "IORE" submodel for metabolites, fitting with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "transform_rates = TRUE" (the default) often leads to failures of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' numerical ODE solver. In this situation it may help to switch off the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' internal rate transformation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [summary.mkinfit], [plot.mkinfit], [parms] and [lrtest].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Comparisons of models fitted to the same data can be made using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Fitting of several models to several datasets in a single call to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Rocke DM and Lorenzato S (1995) A two-component model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for measurement error in analytical chemistry. *Technometrics* 37(2), 176-184.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Degradation Data. *Environments* 6(12) 124</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \doi{10.3390/environments6120124}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Use shorthand notation for parent only degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # One parent compound, one metabolite, both single first order.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We remove zero values from FOCUS dataset D in order to avoid warnings</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS_D <- subset(FOCUS_2006_D, value != 0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Use mkinsub for convenience in model formulation. Pathway to sink included per default.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">183</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Fit the model quietly to the FOCUS example dataset D using defaults</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_sep(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # As lower parent values appear to have lower variance, we try an alternative error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.tc <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">192</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This avoids the warning, and the likelihood ratio test confirms it is preferable</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(fit.tc, fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can also allow for different variances of parent and metabolite as error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">195</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.obs <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "obs")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The two-component error model has significantly higher likelihood</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(fit.obs, fit.tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fit.tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(fit.tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can show a quick (only one replication) benchmark for this case, as we</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # have several alternative solution methods for the model. We skip</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # uncompiled deSolve, as it is so slow. More benchmarks are found in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">204</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # benchmark vignette</pre> + </td> + </tr> + <tr class="never"> + <td class="num">205</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if(require(rbenchmark)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' benchmark(replications = 1, order = "relative", columns = c("test", "relative", "elapsed"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deSolve_compiled = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">209</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve", use_compiled = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' eigen = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "eigen"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = "tc",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "analytical"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">217</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOMC_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("FOMC", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">222</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">223</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Again, we get a warning and try a more sophisticated error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.FOMC_SFO.tc <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This model has a higher likelihood, but not significantly so</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(fit.tc, fit.FOMC_SFO.tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Also, the missing standard error for log_beta and the t-tests for alpha</pre> + </td> + </tr> + <tr class="never"> + <td class="num">228</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # and beta indicate overparameterisation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">229</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(fit.FOMC_SFO.tc, data = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can easily use starting parameters from the parent only fit (only for illustration)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms.ini = fit.FOMC$bparms.ode, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">235</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">237</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinfit <- function(mkinmod, observed,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.ini = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">239</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">240</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> err.ini = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_parms = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_initials = names(mkinmod$diffs)[-1],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">243</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> from_max_mean = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = c("auto", "analytical", "eigen", "deSolve"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">245</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method.ode = "lsoda",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> use_compiled = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">247</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> control = list(eval.max = 300, iter.max = 200),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">248</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">249</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> quiet = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">251</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = 1e-8, rtol = 1e-10,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">252</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model = c("const", "obs", "tc"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">253</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep", "IRLS", "OLS"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> reweight.tol = 1e-8, reweight.max.iter = 10,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> trace_parms = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> test_residuals = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">259</td> + <td class="coverage">9202<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- match.call()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">261</td> + <td class="coverage">9202<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> summary_warnings <- character()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">263</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Derive the name used for the model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">9202<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.character(mkinmod)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">265</td> + <td class="coverage">4009<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod_name <- mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">266</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">5193<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(mkinmod$name)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">5071<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod_name <- deparse(substitute(mkinmod))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">269</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">270</td> + <td class="coverage">18<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod_name <- mkinmod$name</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">272</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">273</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">274</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check mkinmod and generate a model for the variable whith the highest value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">275</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # if a suitable string is given</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">276</td> + <td class="coverage">9098<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE", "logistic")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">277</td> + <td class="coverage">9098<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(mkinmod, "mkinmod")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">4009<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> presumed_parent_name = observed[which.max(observed$value), "name"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">4009<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod[[1]] %in% parent_models_available) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">3905<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> speclist <- list(list(type = mkinmod, sink = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">3905<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(speclist) <- presumed_parent_name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">282</td> + <td class="coverage">3905<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod <- mkinmod(speclist = speclist, use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">283</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Argument mkinmod must be of class mkinmod or a string containing one of\n ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(parent_models_available, collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">286</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">287</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">288</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">289</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the names of the state variables in the model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">290</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(mkinmod$diffs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">291</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">292</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the names of observed variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">293</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- names(mkinmod$spec)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">294</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">295</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Subset observed data with names of observed data in the model and remove NA values</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">296</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- subset(observed, name %in% obs_vars)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">297</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- subset(observed, !is.na(value))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">299</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Also remove zero values to avoid instabilities (e.g. of the 'tc' error model)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">300</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(observed$value == 0)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">301</td> + <td class="coverage">529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> zero_warning <- "Observations with value of zero were removed from the data"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">302</td> + <td class="coverage">529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> summary_warnings <- c(summary_warnings, Z = zero_warning)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">303</td> + <td class="coverage">529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warning(zero_warning)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">304</td> + <td class="coverage">529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- subset(observed, value != 0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">305</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">306</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">307</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Sort observed values for efficient analytical predictions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">308</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$name <- ordered(observed$name, levels = obs_vars)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">309</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- observed[order(observed$name, observed$time), ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">310</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">311</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Obtain data for decline from maximum mean value if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">312</td> + <td class="coverage">8994<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (from_max_mean) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">313</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # This is only used for simple decline models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">314</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) > 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">315</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Decline from maximum is only implemented for models with a single observed variable")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">316</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$name <- as.character(observed$name)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">317</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">318</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> means <- aggregate(value ~ time, data = observed, mean, na.rm=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">319</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_of_max <- means[which.max(means$value), "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">320</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- subset(observed, time >= t_of_max)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">321</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$time <- observed$time - t_of_max</pre> + </td> + </tr> + <tr class="never"> + <td class="num">322</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">323</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">324</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Number observations used for fitting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">325</td> + <td class="coverage">8841<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_observed <- nrow(observed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">326</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">327</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define starting values for parameters where not specified by the user</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">328</td> + <td class="coverage">8371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parms.ini[[1]] == "auto") parms.ini = vector()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">329</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">330</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Override parms.ini for parameters given as a numeric vector in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">331</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # fixed_parms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">332</td> + <td class="coverage">8841<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.numeric(fixed_parms)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">333</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_parm_names <- names(fixed_parms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">334</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.ini[fixed_parm_names] <- fixed_parms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">335</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_parms <- fixed_parm_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">336</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">337</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">338</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Warn for inital parameter specifications that are not in the model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">339</td> + <td class="coverage">8841<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> wrongpar.names <- setdiff(names(parms.ini), mkinmod$parms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">340</td> + <td class="coverage">8841<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(wrongpar.names) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">341</td> + <td class="coverage">257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">342</td> + <td class="coverage">257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> " not used in the model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">343</td> + <td class="coverage">257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.ini <- parms.ini[setdiff(names(parms.ini), wrongpar.names)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">344</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">345</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">346</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Warn that the sum of formation fractions may exceed one if they are not</pre> + </td> + </tr> + <tr class="never"> + <td class="num">347</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # fitted in the transformed way</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">348</td> + <td class="coverage">8841<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod$use_of_ff == "max" & transform_fractions == FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">349</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warning("The sum of formation fractions may exceed one if you do not use ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">350</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "transform_fractions = TRUE." )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">351</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">352</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Stop if formation fractions are not transformed and we have no sink</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">353</td> + <td class="coverage">716<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod$spec[[box]]$sink == FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">354</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("If formation fractions are not transformed during the fitting, ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">355</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "it is not supported to turn off pathways to sink.\n ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">356</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Consider turning on the transformation of formation fractions or ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">357</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "setting up a model with use_of_ff = 'min'.\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">358</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">359</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">360</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">361</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">362</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not allow fixing formation fractions if we are using the ilr transformation,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">363</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # this is not supported</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">364</td> + <td class="coverage">8737<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transform_fractions == TRUE && length(fixed_parms) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">365</td> + <td class="coverage">107<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(grepl("^f_", fixed_parms))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">366</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Fixing formation fractions is not supported when using the ilr ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">367</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "transformation.")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">368</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">369</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">370</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">371</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set initial parameter values, including a small increment (salt)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">372</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # to avoid linear dependencies (singular matrix) in Eigenvalue based solutions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">373</td> + <td class="coverage">8633<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_salt = 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">374</td> + <td class="coverage">8633<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> defaultpar.names <- setdiff(mkinmod$parms, names(parms.ini))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">375</td> + <td class="coverage">8633<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (parmname in defaultpar.names) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">376</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Default values for rate constants, depending on the parameterisation</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">377</td> + <td class="coverage">20999<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (grepl("^k", parmname)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">378</td> + <td class="coverage">15908<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.ini[parmname] = 0.1 + k_salt</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">379</td> + <td class="coverage">15908<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_salt = k_salt + 1e-4</pre> + </td> + </tr> + <tr class="never"> + <td class="num">380</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">381</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Default values for rate constants for reversible binding</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">382</td> + <td class="coverage">26<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (grepl("free_bound$", parmname)) parms.ini[parmname] = 0.1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">383</td> + <td class="coverage">26<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (grepl("bound_free$", parmname)) parms.ini[parmname] = 0.02</pre> + </td> + </tr> + <tr class="never"> + <td class="num">384</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Default values for IORE exponents</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">385</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (grepl("^N", parmname)) parms.ini[parmname] = 1.1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">386</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Default values for the FOMC, DFOP and HS models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">387</td> + <td class="coverage">238<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "alpha") parms.ini[parmname] = 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">388</td> + <td class="coverage">238<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "beta") parms.ini[parmname] = 10</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">389</td> + <td class="coverage">1014<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "k1") parms.ini[parmname] = 0.1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">390</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "k2") parms.ini[parmname] = 0.01</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">391</td> + <td class="coverage">30<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "tb") parms.ini[parmname] = 5</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">392</td> + <td class="coverage">984<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "g") parms.ini[parmname] = 0.5</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">393</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "kmax") parms.ini[parmname] = 0.1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">394</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "k0") parms.ini[parmname] = 0.0001</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">395</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parmname == "r") parms.ini[parmname] = 0.2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">396</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">397</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Default values for formation fractions in case they are present</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">398</td> + <td class="coverage">8633<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">399</td> + <td class="coverage">13865<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> origin <- mkinmod$map[[obs_var]][[1]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">400</td> + <td class="coverage">13865<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names <- mkinmod$parms[grep(paste0("^f_", origin), mkinmod$parms)]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">401</td> + <td class="coverage">13865<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(f_names) > 0) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">402</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We need to differentiate between default and specified fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">403</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and set the unspecified to 1 - sum(specified)/n_unspecified</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">404</td> + <td class="coverage">3365<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_default_names <- intersect(f_names, defaultpar.names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">405</td> + <td class="coverage">3365<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_specified_names <- setdiff(f_names, defaultpar.names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">406</td> + <td class="coverage">3365<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sum_f_specified = sum(parms.ini[f_specified_names])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">407</td> + <td class="coverage">3365<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (sum_f_specified > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">408</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Starting values for the formation fractions originating from ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">409</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> origin, " sum up to more than 1.")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">410</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">411</td> + <td class="coverage">3260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (mkinmod$spec[[obs_var]]$sink) n_unspecified = length(f_default_names) + 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">412</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">413</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_unspecified = length(f_default_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">414</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">415</td> + <td class="coverage">3261<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.ini[f_default_names] <- (1 - sum_f_specified) / n_unspecified</pre> + </td> + </tr> + <tr class="never"> + <td class="num">416</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">417</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">418</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">419</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set default for state.ini if appropriate</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">420</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_name = names(mkinmod$spec)[[1]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">421</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_time_0 = subset(observed, time == 0 & name == parent_name)$value</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">422</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_time_0_mean = mean(parent_time_0, na.rm = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">423</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.na(parent_time_0_mean)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">424</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_auto = c(100, rep(0, length(mkinmod$diffs) - 1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">425</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">426</td> + <td class="coverage">8527<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_auto = c(parent_time_0_mean, rep(0, length(mkinmod$diffs) - 1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">427</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">428</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(state.ini_auto) <- mod_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">429</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">430</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (state.ini[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">431</td> + <td class="coverage">8316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_used <- state.ini_auto</pre> + </td> + </tr> + <tr class="never"> + <td class="num">432</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">433</td> + <td class="coverage">213<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_used <- state.ini_auto</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">434</td> + <td class="coverage">213<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_good <- intersect(names(mkinmod$diffs), names(state.ini))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">435</td> + <td class="coverage">213<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini_used[state.ini_good] <- state.ini[state.ini_good]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">436</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">437</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini <- state.ini_used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">438</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">439</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Name the inital state variable values if they are not named yet</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">440</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if(is.null(names(state.ini))) names(state.ini) <- mod_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">441</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">442</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform initial parameter values for fitting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">443</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms.ini <- transform_odeparms(parms.ini, mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">444</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">445</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">446</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">447</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Parameters to be optimised:</pre> + </td> + </tr> + <tr class="never"> + <td class="num">448</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Kinetic parameters in parms.ini whose names are not in fixed_parms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">449</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.fixed <- parms.ini[fixed_parms]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">450</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.optim <- parms.ini[setdiff(names(parms.ini), fixed_parms)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">451</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">452</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms.fixed <- transform_odeparms(parms.fixed, mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">453</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">454</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">455</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms.optim <- transform_odeparms(parms.optim, mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">456</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">457</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">458</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">459</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Inital state variables in state.ini whose names are not in fixed_initials</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">460</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.fixed <- state.ini[fixed_initials]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">461</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.optim <- state.ini[setdiff(names(state.ini), fixed_initials)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">462</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">463</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Preserve names of state variables before renaming initial state variable</pre> + </td> + </tr> + <tr class="never"> + <td class="num">464</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">465</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.optim.boxnames <- names(state.ini.optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">466</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.fixed.boxnames <- names(state.ini.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">467</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(state.ini.optim) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">468</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(state.ini.optim) <- paste(names(state.ini.optim), "0", sep="_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">469</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">470</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(state.ini.fixed) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">471</td> + <td class="coverage">4509<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(state.ini.fixed) <- paste(names(state.ini.fixed), "0", sep="_")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">472</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">473</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">474</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Decide if the solution of the model can be based on a simple analytical</pre> + </td> + </tr> + <tr class="never"> + <td class="num">475</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # formula, the spectral decomposition of the matrix (fundamental system)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">476</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # or a numeric ode solver from the deSolve package</pre> + </td> + </tr> + <tr class="never"> + <td class="num">477</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Prefer deSolve over eigen if a compiled model is present and use_compiled</pre> + </td> + </tr> + <tr class="never"> + <td class="num">478</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # is not set to FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">479</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = match.arg(solution_type)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">480</td> + <td class="coverage">8529<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "analytical" && !is.function(mkinmod$deg_func))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">481</td> + <td class="coverage">105<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Analytical solution not implemented for this model.")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">482</td> + <td class="coverage">8424<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "eigen" && !is.matrix(mkinmod$coefmat))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">483</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Eigenvalue based solution not possible, coefficient matrix not present.")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">484</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">485</td> + <td class="coverage">6190<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(mkinmod$spec) == 1 || is.function(mkinmod$deg_func)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">486</td> + <td class="coverage">5434<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "analytical"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">487</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">488</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">489</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "deSolve"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">490</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">491</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.matrix(mkinmod$coefmat)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">492</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "eigen"</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">493</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (max(observed$value, na.rm = TRUE) < 0.1) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">494</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The combination of small observed values (all < 0.1) and solution_type = eigen is error-prone")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">495</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">496</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">497</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "deSolve"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">498</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">499</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">500</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">501</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">502</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">503</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get native symbol before iterations info for speed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">504</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">505</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "deSolve" & use_compiled[1] != FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">506</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinmod[["symbols"]] <- try(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">507</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deSolve::checkDLL(dllname = mkinmod$dll_info[["name"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">508</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = "diffs", initfunc = "initpar",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">509</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> jacfunc = NULL, nout = 0, outnames = NULL))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">510</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(mkinmod[["symbols"]], "try-error")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">511</td> + <td class="coverage">2144<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">512</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">513</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">514</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">515</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the error model and the algorithm for fitting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">516</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod <- match.arg(error_model)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">517</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model_algorithm = match.arg(error_model_algorithm)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">518</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "OLS") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">519</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod != "const") stop("OLS is only appropriate for constant variance")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">520</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">521</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">522</td> + <td class="coverage">6692<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model_algorithm = switch(err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">523</td> + <td class="coverage">6692<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "OLS", obs = "d_3", tc = "d_3")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">524</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">525</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparm_names <- switch(err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">526</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "const" = "sigma",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">527</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "obs" = paste0("sigma_", obs_vars),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">528</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "tc" = c("sigma_low", "rsd_high"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">529</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparm_names_optim <- if (error_model_algorithm == "OLS") NULL else errparm_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">530</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">531</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define starting values for the error model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">532</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err.ini[1] != "auto") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">533</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(names(err.ini), errparm_names)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">534</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please supply initial values for error model components ", paste(errparm_names, collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">535</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">536</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> errparms = err.ini</pre> + </td> + </tr> + <tr class="never"> + <td class="num">537</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">538</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">539</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "const") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">540</td> + <td class="coverage">6410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms = 3</pre> + </td> + </tr> + <tr class="never"> + <td class="num">541</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">542</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "obs") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">543</td> + <td class="coverage">317<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms = rep(3, length(obs_vars))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">544</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">545</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">546</td> + <td class="coverage">1593<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- c(sigma_low = 0.1, rsd_high = 0.1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">547</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">548</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(errparms) <- errparm_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">549</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">550</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "OLS") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">551</td> + <td class="coverage">6410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_optim <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">552</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">553</td> + <td class="coverage">1910<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_optim <- errparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">554</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">555</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">556</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Unique outtimes for model solution.</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">557</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes <- sort(unique(observed$time))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">558</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">559</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define the objective function for optimisation, including (back)transformations</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">560</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_function <- function(P, trans = TRUE, OLS = FALSE, fixed_degparms = FALSE, fixed_errparms = FALSE, update_data = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">561</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">562</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> assign("calls", calls + 1, inherits = TRUE) # Increase the model solution counter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">563</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">564</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #browser()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">565</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">566</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Trace parameter values if requested and if we are actually optimising</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">567</td> + <td class="coverage">3224<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(trace_parms & update_data) cat(format(P, width = 10, digits = 6), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">568</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">569</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Determine local parameter values for the cost estimation</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">570</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.numeric(fixed_degparms)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">571</td> + <td class="coverage">94746<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_degparms <- fixed_degparms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">572</td> + <td class="coverage">94746<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_errparms <- P</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">573</td> + <td class="coverage">94746<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_fixed = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">574</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">575</td> + <td class="coverage">3991822<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_fixed = FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">576</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">577</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">578</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.numeric(fixed_errparms)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">579</td> + <td class="coverage">4725<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_degparms <- P</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">580</td> + <td class="coverage">4725<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_errparms <- fixed_errparms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">581</td> + <td class="coverage">4725<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_fixed = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">582</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">583</td> + <td class="coverage">4081843<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_fixed = FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">584</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">585</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">586</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (OLS) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">587</td> + <td class="coverage">1063145<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_degparms <- P</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">588</td> + <td class="coverage">1063145<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_errparms <- numeric(0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">589</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">590</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">591</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!OLS & !degparms_fixed & !errparms_fixed) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">592</td> + <td class="coverage">2923952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_degparms <- P[1:(length(P) - length(errparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">593</td> + <td class="coverage">2923952<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost_errparms <- P[(length(cost_degparms) + 1):length(P)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">594</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">595</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">596</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Initial states for t0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">597</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(state.ini.optim) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">598</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- c(cost_degparms[1:length(state.ini.optim)], state.ini.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">599</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">600</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">601</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- state.ini.fixed</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">602</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini) <- state.ini.fixed.boxnames</pre> + </td> + </tr> + <tr class="never"> + <td class="num">603</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">604</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">605</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms.optim <- cost_degparms[(length(state.ini.optim) + 1):length(cost_degparms)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">606</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">607</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (trans == TRUE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">608</td> + <td class="coverage">2580794<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- c(odeparms.optim, transparms.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">609</td> + <td class="coverage">2580794<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- backtransform_odeparms(odeparms, mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">610</td> + <td class="coverage">2580794<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">611</td> + <td class="coverage">2580794<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">612</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">613</td> + <td class="coverage">1505774<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- c(odeparms.optim, parms.fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">614</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">615</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">616</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Solve the system with current parameter values</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">617</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "analytical") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">618</td> + <td class="coverage">2562380<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$predicted <- mkinmod$deg_func(observed, odeini, parms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">619</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">620</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- mkinpredict(mkinmod, parms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">621</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini, outtimes,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">622</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">623</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_compiled = use_compiled,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">624</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = use_symbols,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">625</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method.ode = method.ode,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">626</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = atol, rtol = rtol,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">627</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">628</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">629</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed_index <- cbind(as.character(observed$time), as.character(observed$name))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">630</td> + <td class="coverage">1524188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$predicted <- out[observed_index]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">631</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">632</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">633</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define standard deviation for each observation</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">634</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "const") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">635</td> + <td class="coverage">2789021<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$std <- if (OLS) NA else cost_errparms["sigma"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">636</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">637</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "obs") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">638</td> + <td class="coverage">366137<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> std_names <- paste0("sigma_", observed$name)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">639</td> + <td class="coverage">366137<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$std <- cost_errparms[std_names]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">640</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">641</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">642</td> + <td class="coverage">931410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed$std <- sqrt(cost_errparms["sigma_low"]^2 + observed$predicted^2 * cost_errparms["rsd_high"]^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">643</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">644</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">645</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Calculate model cost</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">646</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (OLS) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">647</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Cost is the sum of squared residuals</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">648</td> + <td class="coverage">1063145<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost <- with(observed, sum((value - predicted)^2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">649</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">650</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Cost is the negative log-likelihood</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">651</td> + <td class="coverage">3023423<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost <- - with(observed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">652</td> + <td class="coverage">3023423<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sum(dnorm(x = value, mean = predicted, sd = std, log = TRUE)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">653</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">654</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">655</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We update the current cost and data during the optimisation, not</pre> + </td> + </tr> + <tr class="never"> + <td class="num">656</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # during hessian calculations</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">657</td> + <td class="coverage">4086568<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (update_data) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">658</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">659</td> + <td class="coverage">1622188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> assign("current_data", observed, inherits = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">660</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">661</td> + <td class="coverage">1622188<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (cost < cost.current) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">662</td> + <td class="coverage">594930<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> assign("cost.current", cost, inherits = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">663</td> + <td class="coverage">1768<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">664</td> + <td class="coverage">1768<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> " at call ", calls, ": ", signif(cost.current, 6), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">665</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">666</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">667</td> + <td class="coverage">4086415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(cost)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">668</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">669</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">670</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names_optim <- c(names(state.ini.optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">671</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(transparms.optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">672</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparm_names_optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">673</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_optim <- length(names_optim)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">674</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">675</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define lower and upper bounds other than -Inf and Inf for parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">676</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # for which no internal transformation is requested in the call to mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">677</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and for optimised error model parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">678</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower <- rep(-Inf, n_optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">679</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper <- rep(Inf, n_optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">680</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(lower) <- names(upper) <- names_optim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">681</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">682</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # IORE exponents are not transformed, but need a lower bound</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">683</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> index_N <- grep("^N", names(lower))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">684</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[index_N] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">685</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">686</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!transform_rates) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">687</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> index_k <- grep("^k_", names(lower))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">688</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[index_k] <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">689</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> index_k__iore <- grep("^k__iore_", names(lower))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">690</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[index_k__iore] <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">691</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2", "tb", "r"), names(lower))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">692</td> + <td class="coverage">553<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[other_rate_parms] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">693</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">694</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">695</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!transform_fractions) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">696</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> index_f <- grep("^f_", names(upper))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">697</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[index_f] <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">698</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper[index_f] <- 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">699</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> other_fraction_parms <- intersect(c("g"), names(upper))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">700</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[other_fraction_parms] <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">701</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper[other_fraction_parms] <- 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">702</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">703</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">704</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "const") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">705</td> + <td class="coverage">6410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm != "OLS") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">706</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lower["sigma"] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">707</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">708</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">709</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "obs") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">710</td> + <td class="coverage">317<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> index_sigma <- grep("^sigma_", names(lower))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">711</td> + <td class="coverage">317<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower[index_sigma] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">712</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">713</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">714</td> + <td class="coverage">1593<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower["sigma_low"] <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">715</td> + <td class="coverage">1593<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower["rsd_high"] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">716</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">717</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">718</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Counter for cost function evaluations</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">719</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> calls = 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">720</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost.current <- Inf</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">721</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_predicted <- NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">722</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> current_data <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">723</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">724</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show parameter names if tracing is requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">725</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(trace_parms) cat(format(names_optim, width = 10), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">726</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">727</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #browser()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">728</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">729</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do the fit and take the time until the hessians are calculated</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">730</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_time <- system.time({</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">731</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- c(state.ini.optim, transparms.optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">732</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_degparms <- length(degparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">733</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms_index <- seq(1, n_degparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">734</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_index <- seq(n_degparms + 1, length.out = length(errparms))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">735</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">736</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "d_3") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">737</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Directly optimising the complete model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">738</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.start <- c(degparms, errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">739</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_direct <- try(nlminb(parms.start, cost_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">740</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(parms.start)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">741</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(parms.start)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">742</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> control = control, ...))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">743</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(fit_direct, "try-error")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">744</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_direct$logLik <- - cost.current</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">745</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost.current <- Inf # reset to avoid conflict with the OLS step</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">746</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_direct <- current_data # We need this later if it was better</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">747</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> direct_failed = FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">748</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">749</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> direct_failed = TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">750</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">751</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">752</td> + <td class="coverage">8320<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm != "direct") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">753</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Ordinary least squares optimisation")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">754</td> + <td class="coverage">7884<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(degparms, cost_function, control = control,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">755</td> + <td class="coverage">7884<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(degparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">756</td> + <td class="coverage">7884<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(degparms)], OLS = TRUE, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">757</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">758</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">759</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the maximum likelihood estimate for sigma at the optimum parameter values</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">760</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> current_data$residual <- current_data$value - current_data$predicted</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">761</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_mle <- sqrt(sum(current_data$residual^2)/nrow(current_data))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">762</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">763</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Use that estimate for the constant variance, or as first guess if err_mod = "obs"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">764</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod != "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">765</td> + <td class="coverage">6327<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms[names(errparms)] <- sigma_mle</pre> + </td> + </tr> + <tr class="never"> + <td class="num">766</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">767</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$par <- c(fit$par, errparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">768</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">769</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost.current <- cost_function(c(degparms, errparms), OLS = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">770</td> + <td class="coverage">7731<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$logLik <- - cost.current</pre> + </td> + </tr> + <tr class="never"> + <td class="num">771</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">772</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm %in% c("threestep", "fourstep", "d_3")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">773</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Optimising the error model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">774</td> + <td class="coverage">1096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(errparms, cost_function, control = control,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">775</td> + <td class="coverage">1096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(errparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">776</td> + <td class="coverage">1096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(errparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">777</td> + <td class="coverage">1096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_degparms = degparms, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">778</td> + <td class="coverage">1096<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">779</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">780</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "fourstep") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">781</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Optimising the degradation model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">782</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(degparms, cost_function, control = control,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">783</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(degparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">784</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(degparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">785</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_errparms = errparms, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">786</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">787</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">788</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm %in%</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">789</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c("direct", "twostep", "threestep", "fourstep", "d_3")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">790</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Optimising the complete model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">791</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.start <- c(degparms, errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">792</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(parms.start, cost_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">793</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(parms.start)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">794</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(parms.start)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">795</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> control = control, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">796</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- fit$par[degparms_index]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">797</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- fit$par[errparms_index]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">798</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$logLik <- - cost.current</pre> + </td> + </tr> + <tr class="never"> + <td class="num">799</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">800</td> + <td class="coverage">1721<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model_algorithm == "d_3") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">801</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_3_messages = c(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">802</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> direct_failed = "Direct fitting failed, results of three-step fitting are returned",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">803</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> same = "Direct fitting and three-step fitting yield approximately the same likelihood",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">804</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> threestep = "Three-step fitting yielded a higher likelihood than direct fitting",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">805</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> direct = "Direct fitting yielded a higher likelihood than three-step fitting")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">806</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (direct_failed) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">807</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message(d_3_messages["direct_failed"])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">808</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> fit$d_3_message <- d_3_messages["direct_failed"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">809</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">810</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rel_diff <- abs((fit_direct$logLik - fit$logLik))/-mean(c(fit_direct$logLik, fit$logLik))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">811</td> + <td class="coverage">471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (rel_diff < 0.0001) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">812</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message(d_3_messages["same"])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">813</td> + <td class="coverage">240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$d_3_message <- d_3_messages["same"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">814</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">815</td> + <td class="coverage">231<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (fit$logLik > fit_direct$logLik) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">816</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message(d_3_messages["threestep"])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">817</td> + <td class="coverage">15<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$d_3_message <- d_3_messages["threestep"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">818</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">819</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message(d_3_messages["direct"])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">820</td> + <td class="coverage">216<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- fit_direct</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">821</td> + <td class="coverage">216<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$d_3_message <- d_3_messages["direct"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">822</td> + <td class="coverage">216<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- fit$par[degparms_index]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">823</td> + <td class="coverage">216<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- fit$par[errparms_index]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">824</td> + <td class="coverage">216<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> current_data <- data_direct</pre> + </td> + </tr> + <tr class="never"> + <td class="num">825</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">826</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">827</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">828</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">829</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">830</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (err_mod != "const" & error_model_algorithm == "IRLS") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">831</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> reweight.diff <- 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">832</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.iter <- 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">833</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_last <- errparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">834</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">835</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> while (reweight.diff > reweight.tol &</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">836</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.iter < reweight.max.iter) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">837</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">838</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Optimising the error model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">839</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(errparms, cost_function, control = control,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">840</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(errparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">841</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(errparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">842</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_degparms = degparms, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">843</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">844</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">845</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Optimising the degradation model")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">846</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- nlminb(degparms, cost_function, control = control,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">847</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower[names(degparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">848</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper[names(degparms)],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">849</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_errparms = errparms, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">850</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparms <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">851</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">852</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> reweight.diff <- dist(rbind(errparms, errparms_last))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">853</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms_last <- errparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">854</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">855</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$par <- c(fit$par, errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">856</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost.current <- cost_function(c(degparms, errparms), OLS = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">857</td> + <td class="coverage">756<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$logLik <- - cost.current</pre> + </td> + </tr> + <tr class="never"> + <td class="num">858</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">859</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">860</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">861</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim_hessian <- length(c(degparms, errparms))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">862</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">863</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$hessian <- try(numDeriv::hessian(cost_function, c(degparms, errparms), OLS = FALSE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">864</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_data = FALSE), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">865</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit$hessian, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">866</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> fit$hessian <- matrix(NA, nrow = dim_hessian, ncol = dim_hessian)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">867</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">868</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(fit$hessian) <- list(names(c(degparms, errparms)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">869</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(c(degparms, errparms)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">870</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">871</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Backtransform parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">872</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms.optim = backtransform_odeparms(degparms, mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">873</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">874</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">875</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms.fixed = c(state.ini.fixed, parms.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">876</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms.all = c(bparms.optim, parms.fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">877</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">878</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$hessian_notrans <- try(numDeriv::hessian(cost_function, c(bparms.optim, errparms),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">879</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> OLS = FALSE, trans = FALSE, update_data = FALSE), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">880</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit$hessian_notrans, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">881</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> fit$hessian_notrans <- matrix(NA, nrow = dim_hessian, ncol = dim_hessian)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">882</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">883</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(fit$hessian_notrans) <- list(names(c(bparms.optim, errparms)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">884</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(c(bparms.optim, errparms)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">885</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">886</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">887</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$call <- call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">888</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">889</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$error_model_algorithm <- error_model_algorithm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">890</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">891</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (fit$convergence != 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">892</td> + <td class="coverage">108<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> convergence_warning = paste0("Optimisation did not converge:\n", fit$message)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">893</td> + <td class="coverage">108<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> summary_warnings <- c(summary_warnings, C = convergence_warning)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">894</td> + <td class="coverage">108<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warning(convergence_warning)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">895</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">896</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(!quiet) message("Optimisation successfully terminated.\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">897</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">898</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">899</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We need to return some more data for summary and plotting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">900</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$solution_type <- solution_type</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">901</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$transform_rates <- transform_rates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">902</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$transform_fractions <- transform_fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">903</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$reweight.tol <- reweight.tol</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">904</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$reweight.max.iter <- reweight.max.iter</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">905</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$control <- control</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">906</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$calls <- calls</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">907</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$time <- fit_time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">908</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">909</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We also need the model and a model name for summary and plotting,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">910</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # but without symbols because they could become invalid</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">911</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$symbols <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">912</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$mkinmod <- mkinmod</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">913</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$mkinmod$name <- mkinmod_name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">914</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$obs_vars <- obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">915</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">916</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Residual sum of squares as a function of the fitted parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">917</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$rss <- function(P) cost_function(P, OLS = TRUE, update_data = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">918</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">919</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Log-likelihood with possibility to fix degparms or errparms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">920</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$ll <- function(P, fixed_degparms = FALSE, fixed_errparms = FALSE, trans = FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">921</td> + <td class="coverage">547080<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> - cost_function(P, trans = trans, fixed_degparms = fixed_degparms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">922</td> + <td class="coverage">547080<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">923</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">924</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">925</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Collect initial parameter values in three dataframes</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">926</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$start <- data.frame(value = c(state.ini.optim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">927</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.optim, errparms_optim))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">928</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$start$type = c(rep("state", length(state.ini.optim)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">929</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rep("deparm", length(parms.optim)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">930</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rep("error", length(errparms_optim)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">931</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">932</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$start_transformed = data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">933</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> value = c(state.ini.optim, transparms.optim, errparms_optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">934</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower = lower,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">935</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = upper)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">936</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">937</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$fixed <- data.frame(value = c(state.ini.fixed, parms.fixed))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">938</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$fixed$type = c(rep("state", length(state.ini.fixed)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">939</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rep("deparm", length(parms.fixed)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">940</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">941</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$data <- data.frame(time = current_data$time,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">942</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> variable = current_data$name,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">943</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed = current_data$value,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">944</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted = current_data$predicted)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">945</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">946</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$data$residual <- fit$data$observed - fit$data$predicted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">947</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">948</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$atol <- atol</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">949</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$rtol <- rtol</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">950</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$err_mod <- err_mod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">951</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">952</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Return different sets of backtransformed parameters for summary and plotting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">953</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$bparms.optim <- bparms.optim</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">954</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$bparms.fixed <- bparms.fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">955</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">956</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Return ode and state parameters for further fitting</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">957</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$bparms.ode <- bparms.all[mkinmod$parms]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">958</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$bparms.state <- c(bparms.all[setdiff(names(bparms.all), names(fit$bparms.ode))],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">959</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">960</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(fit$bparms.state) <- gsub("_0$", "", names(fit$bparms.state))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">961</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">962</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$errparms <- errparms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">963</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$df.residual <- n_observed - length(c(degparms, errparms))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">964</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">965</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Assign the class here so method dispatch works for residuals</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">966</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(fit) <- c("mkinfit")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">967</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">968</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (test_residuals) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">969</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check for normal distribution of residuals</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">970</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$shapiro.p <- shapiro.test(residuals(fit, standardized = TRUE))$p.value</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">971</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (fit$shapiro.p < 0.05) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">972</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> shapiro_warning <- paste("Shapiro-Wilk test for standardized residuals: p = ", signif(fit$shapiro.p, 3))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">973</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> warning(shapiro_warning)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">974</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> summary_warnings <- c(summary_warnings, S = shapiro_warning)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">975</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">976</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">977</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">978</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$summary_warnings <- summary_warnings</pre> + </td> + </tr> + <tr class="never"> + <td class="num">979</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">980</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$date <- date()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">981</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$version <- as.character(utils::packageVersion("mkin"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">982</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$Rversion <- paste(R.version$major, R.version$minor, sep=".")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">983</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">984</td> + <td class="coverage">8167<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">985</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/illparms.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Method to get the names of ill-defined parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The method for generalised nonlinear regression fits as obtained</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' with [mkinfit] and [mmkin] checks if the degradation parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' pass the Wald test (in degradation kinetics often simply called t-test) for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' significant difference from zero. For this test, the parameterisation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' without parameter transformations is used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The method for hierarchical model fits, also known as nonlinear</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mixed-effects model fits as obtained with [saem] and [mhmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' checks if any of the confidence intervals for the random</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' effects expressed as standard deviations include zero, and if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the confidence intervals for the error model parameters include</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The object to investigate</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x The object to be printed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param conf.level The confidence level for checking p values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For potential future extensions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param random For hierarchical fits, should random effects be tested?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param errmod For hierarchical fits, should error model parameters be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' tested?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param slopes For hierarchical [saem] fits using saemix as backend,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' should slope parameters in the covariate model(starting with 'beta_') be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' tested?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return For [mkinfit] or [saem] objects, a character vector of parameter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names. For [mmkin] or [mhmkin] objects, a matrix like object of class</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'illparms.mmkin' or 'illparms.mhmkin'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note All return objects have printing methods. For the single fits, printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' does not output anything in the case no ill-defined parameters are found.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">illparms <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">2471<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("illparms", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">illparms.mkinfit <- function(object, conf.level = 0.95, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> p_values <- suppressWarnings(summary(object)$bpar[, "Pr(>t)"])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na <- is.na(p_values)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> failed <- p_values > 1 - conf.level</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret <- names(parms(object))[na | failed]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(ret) <- "illparms.mkinfit"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ret)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.illparms.mkinfit <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">190<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">190<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(x) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">56</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(as.character(x))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c("SFO", "FOMC"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list("FOCUS A" = FOCUS_2006_A,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "FOCUS C" = FOCUS_2006_C),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(fits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">illparms.mmkin <- function(object, conf.level = 0.95, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(fit) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">74</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit, "try-error")) return("E")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill <- illparms(fit, conf.level = conf.level)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ill) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(paste(ill, collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return("")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(result) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(result) <- dimnames(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "illparms.mmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.illparms.mmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x, quote = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">illparms.saem.mmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, slopes = TRUE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object$so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">100</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ints <- intervals(object, conf.level = conf.level)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms <- character(0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (random) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms_random_i <- which(ints$random[, "lower"] < 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms_random <- rownames(ints$random)[ill_parms_random_i]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms <- c(ill_parms, ill_parms_random)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (errmod) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms_errmod_i <- which(ints$errmod[, "lower"] < 0 & ints$errmod[, "upper"] > 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms_errmod <- rownames(ints$errmod)[ill_parms_errmod_i]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms <- c(ill_parms, ill_parms_errmod)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (slopes) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">115</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(object$so)) stop("Slope testing is only implemented for the saemix backend")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> slope_names <- grep("^beta_", object$so@model@name.fixed, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ci <- object$so@results@conf.int</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(ci) <- ci$name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> slope_ci <- ci[slope_names, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms_slopes <- slope_ci[, "lower"] < 0 & slope_ci[, "upper"] > 0</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill_parms <- c(ill_parms, slope_names[ill_parms_slopes])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(ill_parms) <- "illparms.saem.mmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">2091<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ill_parms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.illparms.saem.mmkin <- print.illparms.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">illparms.mhmkin <- function(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object[[1]], "saem.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> check_failed <- function(x) if (inherits(x$so, "try-error")) TRUE else FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(fit) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">1484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (check_failed(fit)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">141</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return("E")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">1484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(fit$FIM_failed) &&</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "random effects and error model parameters" %in% fit$FIM_failed) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">145</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return("NA")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">1484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ill <- illparms(fit, conf.level = conf.level, random = random, errmod = errmod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">1484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ill) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">1000<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(paste(ill, collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">484<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return("")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(result) <- dim(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(result) <- dimnames(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "illparms.mhmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">371<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname illparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.illparms.mhmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x, quote = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/plot.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("type", "variable", "observed"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot the observed data and the fitted model of an mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Solves the differential equations with the optimised and fixed parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from a previous successful call to \code{\link{mkinfit}} and plots the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed data together with the solution of the fitted model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' latex is being used for the formatting of the chi2 error level, if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{show_errmin = TRUE}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @aliases plot.mkinfit plot_sep plot_res plot_err</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x Alias for fit introduced for compatibility with the generic S3</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fit An object of class \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param obs_vars A character vector of names of the observed variables for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' which the data and the model should be plotted. Defauls to all observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables in the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlab Label for the x axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ylab Label for the y axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlim Plot range in x direction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ylim Plot range in y direction. If given as a list, plot ranges</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for the different plot rows can be given for row layout.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param col_obs Colors used for plotting the observed data and the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' corresponding model prediction lines.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pch_obs Symbols to be used for plotting the data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lty_obs Line types to be used for the model predictions.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param add Should the plot be added to an existing plot?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param legend Should a legend be added to the plot?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param show_residuals Should residuals be shown? If only one plot of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits is shown, the residual plot is in the lower third of the plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Otherwise, i.e. if "sep_obs" is given, the residual plots will be located</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to the right of the plots of the fitted curves. If this is set to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'standardized', a plot of the residuals divided by the standard deviation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' given by the fitted error model will be shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param standardized When calling 'plot_res', should the residuals be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' standardized in the residual plot?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param show_errplot Should squared residuals and the error model be shown?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If only one plot of the fits is shown, this plot is in the lower third of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be located to the right of the plots of the fitted curves.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param maxabs Maximum absolute value of the residuals. This is used for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' scaling of the y axis and defaults to "auto".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param sep_obs Should the observed variables be shown in separate subplots?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If yes, residual plots requested by "show_residuals" will be shown next</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to, not below the plot of the fits.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rel.height.middle The relative height of the middle plot, if more</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' than two rows of plots are shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param row_layout Should we use a row layout where the residual plot or the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' error model plot is shown to the right?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lpos Position(s) of the legend(s). Passed to \code{\link{legend}} as</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the first argument. If not length one, this should be of the same length</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as the obs_var argument.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param inset Passed to \code{\link{legend}} if applicable.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param show_errmin Should the FOCUS chi2 error value be shown in the upper</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' margin of the plot?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param errmin_digits The number of significant digits for rounding the FOCUS</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' chi2 error percentage.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param frame Should a frame be drawn around the plots?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments passed to \code{\link{plot}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @import graphics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom grDevices dev.cur</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # One parent compound, one metabolite, both single first order, path from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # parent to sink included</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO", full = "Metabolite M1" ))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(fit, standardized = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_err(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Show the observed variables separately, with residuals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' show_errmin = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The same can be obtained with less typing, using the convenience function plot_sep</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_sep(fit, lpos = c("topright", "bottomright"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Show the observed variables separately, with the error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c("topright", "bottomright"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' show_errmin = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot.mkinfit <- function(x, fit = x,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars = names(fit$mkinmod$map),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "Time", ylab = "Residue",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = range(fit$data$time),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = "default",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> col_obs = 1:length(obs_vars),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_obs = col_obs,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> lty_obs = rep(1, length(obs_vars)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> add = FALSE, legend = !add,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> show_residuals = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> show_errplot = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> maxabs = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> sep_obs = FALSE, rel.height.middle = 0.9,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> row_layout = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> lpos = "topright", inset = c(0.05, 0.05),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> show_errmin = FALSE, errmin_digits = 3,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> frame = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(show_residuals, "standardized")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">112</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> show_residuals <- TRUE</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">113</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> standardized <- TRUE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">118</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (add && show_residuals) stop("If adding to an existing plot we can not show residuals")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">119</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (add && show_errplot) stop("If adding to an existing plot we can not show the error model plot")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">120</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_residuals && show_errplot) stop("We can either show residuals over time or the error model plot, not both")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">121</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (add && sep_obs) stop("If adding to an existing plot we can not show observed variables separately")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = fit$solution_type</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.all <- c(fit$bparms.optim, fit$bparms.fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ininames <- c(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(subset(fit$start, type == "state")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(subset(fit$fixed, type == "state")))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- parms.all[ininames]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Order initial state variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini) <- sub("_0", "", names(odeini))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- odeini[names(fit$mkinmod$diffs)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes <- seq(xlim[1], xlim[2], length.out=100)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odenames <- c(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(subset(fit$start, type == "deparm")),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(subset(fit$fixed, type == "deparm")))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- parms.all[odenames]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "deSolve" & !is.null(fit$mkinmod$cf)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit$mkinmod[["symbols"]] <- deSolve::checkDLL(dllname = fit$mkinmod$dll_info[["name"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = "diffs", initfunc = "initpar",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> jacfunc = NULL, nout = 0, outnames = NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- mkinpredict(fit$mkinmod, odeparms, odeini, outtimes,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = solution_type, atol = fit$atol, rtol = fit$rtol)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- as.data.frame(out)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Create a plot layout only if not to be added to an existing plot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # or only a single plot is requested (e.g. by plot.mmkin)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> do_layout = FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">485<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_residuals | sep_obs | show_errplot) do_layout = TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plot_rows = if (sep_obs) length(obs_vars) else 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (do_layout) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Layout should be restored afterwards</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">485<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">165</td> + <td class="coverage">485<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # If the observed variables are shown separately, or if requested, do row layout</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">485<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (sep_obs | row_layout) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row_layout <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plot_cols = if (show_residuals | show_errplot) 2 else 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plots = n_plot_rows * n_plot_cols</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set relative plot heights, so the first and the last plot are the norm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rel.heights <- if (n_plot_rows > 2) c(1, rep(rel.height.middle, n_plot_rows - 2), 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else rep(1, n_plot_rows)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout_matrix = matrix(1:n_plots,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_plot_rows, n_plot_cols, byrow = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout(layout_matrix, heights = rel.heights)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else { # else show residuals in the lower third to keep compatibility</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout(matrix(c(1, 2), 2, 1), heights = c(2, 1.3))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3, 4, 4, 2) + 0.1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">183</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Replicate legend position argument if necessary</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(lpos) == 1) lpos = rep(lpos, n_plot_rows)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Loop over plot rows</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (plot_row in 1:n_plot_rows) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row_obs_vars = if (sep_obs) obs_vars[plot_row] else obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set ylim to sensible default, or to the specified value</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.list(ylim)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">196</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ylim_row <- ylim[[plot_row]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ylim[[1]] == "default") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim_row = c(0, max(c(subset(fit$data, variable %in% row_obs_vars)$observed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> unlist(out[row_obs_vars])), na.rm = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">202</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ylim_row = ylim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">204</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">205</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (row_layout) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for top row of plots when we have more than one row</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Reduce bottom margin by 2.1 - hides x axis legend</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (plot_row == 1 & n_plot_rows > 1) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">210</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3.0, 4.1, 4.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for middle rows of plots, if any</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (plot_row > 1 & plot_row < n_plot_rows) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Reduce top margin by 2 after the first plot as we have no main title,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # reduced plot height, therefore we need rel.height.middle in the layout</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">217</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3.0, 4.1, 2.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for bottom row of plots when we have more than one row</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">415<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (plot_row == n_plot_rows & n_plot_rows > 1) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">222</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Restore bottom margin for last plot to show x axis legend</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">223</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(5.1, 4.1, 2.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set up the main plot if not to be added to an existing plot</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (add == FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type="n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = xlim, ylim = ylim_row,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = xlab, ylab = ylab, frame = frame, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Plot the data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in row_obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">1708<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(subset(fit$data, variable == obs_var, c(time, observed)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">1708<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch = pch_obs[obs_var], col = col_obs[obs_var])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">239</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">240</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Plot the model output</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> matlines(out$time, out[row_obs_vars], col = col_obs[row_obs_vars], lty = lty_obs[row_obs_vars])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (legend == TRUE) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get full names from model definition if they are available</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend_names = lapply(row_obs_vars, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">246</td> + <td class="coverage">900<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(fit$mkinmod$spec[[x]]$full_name))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">410<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.na(fit$mkinmod$spec[[x]]$full_name)) x</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">248</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else fit$mkinmod$spec[[x]]$full_name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">490<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else x</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend(lpos[plot_row], inset= inset, legend = legend_names,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_obs[row_obs_vars], pch = pch_obs[row_obs_vars], lty = lty_obs[row_obs_vars])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">253</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show chi2 error value if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">256</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_errmin) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">257</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(row_obs_vars) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">258</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin_var = row_obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">260</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> errmin_var = "All data"</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">261</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(row_obs_vars) != length(fit$mkinmod$map)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">262</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Showing chi2 error level for all data, but only ",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">263</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> row_obs_vars, " were selected for plotting")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">264</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">266</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">268</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Use LateX if the current plotting device is tikz</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (names(dev.cur()) == "tikz output") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">270</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_text <- paste0("$\\chi^2$ error level = ", chi2, "\\%")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_perc <- paste0(chi2, "%")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">273</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_text <- bquote(chi^2 ~ "error level" == .(chi2_perc))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">274</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">275</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mtext(chi2_text, cex = 0.7, line = 0.4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">276</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">277</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (do_layout & !row_layout) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">279</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(5, 4, 0, 2) + 0.1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">280</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">281</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">282</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show residuals if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">283</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_residuals) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">280<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinresplot(fit, obs_vars = row_obs_vars, standardized = standardized,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">280<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">286</td> + <td class="coverage">280<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend = FALSE, frame = frame, xlab = xlab, xlim = xlim, maxabs = maxabs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">287</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">288</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">289</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Show error model plot if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">290</td> + <td class="coverage">1503<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_errplot) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">291</td> + <td class="coverage">205<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinerrplot(fit, obs_vars = row_obs_vars,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">292</td> + <td class="coverage">205<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">293</td> + <td class="coverage">205<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend = FALSE, frame = frame)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">294</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">295</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">296</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">297</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname plot.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">299</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">300</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot_sep <- function(fit, show_errmin = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">301</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">302</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot.mkinfit(fit, sep_obs = TRUE, show_residuals = show_residuals,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">303</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> show_errmin = show_errmin, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">304</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">305</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">306</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname plot.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">307</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">308</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot_res <- function(fit, sep_obs = FALSE, show_errmin = sep_obs,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">309</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE), ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">310</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">311</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">312</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> show_residuals = ifelse(standardized, "standardized", TRUE),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">313</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row_layout = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">314</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">315</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">316</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname plot.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">317</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">318</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot_err <- function(fit, sep_obs = FALSE, show_errmin = sep_obs, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">319</td> + <td class="coverage">205<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot.mkinfit(fit, sep_obs = sep_obs, show_errmin = show_errmin,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">320</td> + <td class="coverage">205<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> show_errplot = TRUE, row_layout = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">321</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">322</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">323</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot the observed data and the fitted model of an mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">324</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">325</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Deprecated function. It now only calls the plot method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">326</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{plot.mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">327</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">328</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fit an object of class \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">329</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots further arguments passed to \code{\link{plot.mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">330</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">331</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">332</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">333</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinplot <- function(fit, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">334</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">335</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> plot(fit, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">336</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mixed.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Create a mixed effects model from an mmkin row object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom rlang !!!</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An [mmkin] row object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method The method to be used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Currently not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object of class 'mixed.mmkin' which has the observed data in a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' single dataframe which is convenient for plotting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n_biphasic <- 8</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' err_1 = list(const = 1, prop = 0.07)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' DFOP_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("DFOP", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(123456)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' log_sd <- 0.3</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' syn_biphasic_parms <- as.matrix(data.frame(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k1 = rlnorm(n_biphasic, log(0.05), log_sd),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k2 = rlnorm(n_biphasic, log(0.01), log_sd),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' g = plogis(rnorm(n_biphasic, 0, log_sd)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k_m1 = rlnorm(n_biphasic, log(0.002), log_sd)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_biphasic_mean <- lapply(1:n_biphasic,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(i) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0), sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(123456L)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_biphasic <- lapply(ds_biphasic_mean, function(ds) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' add_err(ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n = 1, secondary = "m1")[[1]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, error_model = "tc", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mixed <- mixed(f_mmkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_mixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_mixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mixed <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("mixed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mixed.mmkin <- function(object, method = c("none"), ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">57</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method <- match.arg(method)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_names <- colnames(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- list(mmkin = object, mkinmod = object[[1]]$mkinmod)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (method[1] == "none") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_list <- lapply(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(x) x$data[c("variable", "time", "observed", "predicted", "residual")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds_list) <- ds_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$data <- vctrs::vec_rbind(!!!ds_list, .names_to = "ds")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(res$data)[1:4] <- c("ds", "name", "time", "value")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$data$name <- as.character(res$data$name)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$data$ds <- ordered(res$data$ds, levels = unique(res$data$ds))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized <- unlist(lapply(object, residuals, standardized = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$data$std <- res$data$residual / standardized</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$data$standardized <- standardized</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(res) <- c("mixed.mmkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x A mixed.mmkin object to print</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mixed.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Kinetic model fitted by nonlinear regression to each dataset" )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStructural model:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- x$mmkin[[1]]$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(nrow(x$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$ds)), "datasets\n\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$mmkin, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nMean fitted parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(mean_degparms(x$mmkin), digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/parms.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Extract model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function returns degradation model parameters as well as error</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model parameters per default, in order to avoid working with a fitted model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' without considering the error structure that was assumed for the fit.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A fitted model object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Depending on the object, a numeric vector of fitted model parameters,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mmkin objects with more than one row).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [saem], [multistart]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # mkinfit objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fit, transformed = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds <- lapply(experimental_data_for_UBA_2019[6:10],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(x) subset(x$data[c("name", "time", "value")]))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(ds) <- paste("Dataset", 6:10)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE, cores = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fits["SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fits[, 2])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fits, transformed = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parms <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">91384<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("parms", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transformed Should the parameters be returned as used internally</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' during the optimisation?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param errparms Should the error model parameters be returned</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in addition to the degradation parameters?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname parms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parms.mkinfit <- function(object, transformed = FALSE, errparms = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">88039<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- if (transformed) object$par</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">88039<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else c(object$bparms.optim, object$errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">88039<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!errparms) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">3000<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res[setdiff(names(res), names(object$errparms))]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">85039<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname parms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parms.mmkin <- function(object, transformed = FALSE, errparms = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">265<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">265<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- sapply(object, parms, transformed = transformed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">265<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms = errparms, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">265<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(res) <- colnames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">61</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> res <- list()</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">62</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:nrow(object)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">63</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> res[[i]] <- parms(object[i, ], transformed = transformed,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">64</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> errparms = errparms, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">66</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> names(res) <- rownames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">265<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param exclude_failed For [multistart] objects, should rows for failed fits</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be removed from the returned parameter matrix?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname parms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">parms.multistart <- function(object, exclude_failed = TRUE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- t(sapply(object, parms))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> successful <- which(!is.na(res[, 1]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> first_success <- successful[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(res) <- names(parms(object[[first_success]]))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">80</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (exclude_failed[1]) res <- res[successful, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Fit one or more kinetic models with one or more state variables to one or</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' more datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function calls \code{\link{mkinfit}} on all combinations of models and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' datasets specified in its first two arguments.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param models Either a character vector of shorthand names like</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{c("SFO", "FOMC", "DFOP", "HS", "SFORB")}, or an optionally named</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list of \code{\link{mkinmod}} objects.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param datasets An optionally named list of datasets suitable as observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' data for \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cores The number of cores to be used for multicore processing. This</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is only used when the \code{cluster} argument is \code{NULL}. On Windows</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' machines, cores > 1 is not supported, you need to use the \code{cluster}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' argument to use multiple logical processors. Per default, all cores</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' detected by [parallel::detectCores()] are used, except on Windows where</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the default is 1.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cluster A cluster as returned by \code{\link{makeCluster}} to be used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for parallel execution.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments that will be passed to \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom parallel mclapply parLapply detectCores</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A two-dimensional \code{\link{array}} of \code{\link{mkinfit}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' objects and/or try-errors that can be indexed using the model names for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' first index (row index) and the dataset names for the second index (column</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' index).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plotting.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @keywords optimize</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = mkinsub("SFO", "M2"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = mkinsub("SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = mkinsub("SFO", "M2"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = mkinsub("SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(datasets) <- paste("Dataset", 1:3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time_default</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time_1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(fits.0[["SFO_lin", 2]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # plot.mkinfit handles rows or columns of mmkin result objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits.0[1, ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits.0[1, ], obs_var = c("M1", "M2"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits.0[, 1])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Use double brackets to extract a single mkinfit object, which will be plotted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # by plot.mkinfit and can be plotted using plot_sep</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_sep(fits.0[[1, 1]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Plotting with mmkin (single brackets, extracting an mmkin object) does not</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # allow to plot the observed variables separately</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits.0[1, 1])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # On Windows, we can use multiple cores by making a cluster first</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cl <- parallel::makePSOCKcluster(12)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin(c("SFO", "FOMC", "DFOP"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cluster = cl, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We get false convergence for the FOMC fit to FOCUS_2006_A because this</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # dataset is really SFO, and the FOMC fit is overparameterised</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parallel::stopCluster(cl)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(), cluster = NULL, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- match.call()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE", "logistic")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.m <- length(models)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.d <- length(datasets)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.fits <- n.m * n.d</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_indices <- matrix(1:n.fits, ncol = n.d)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check models and define their names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">4032<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all(sapply(models, function(x) inherits(x, "mkinmod")))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">2323<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all(models %in% parent_models_available)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">50<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please supply models as a list of mkinmod objects or a vector combined of\n ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">50<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(parent_models_available, collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">2273<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(models) <- models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">1087<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(names(models))) names(models) <- as.character(1:n.m)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check datasets and define their names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">1575<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(names(datasets))) names(datasets) <- as.character(1:n.d)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Define names for fit index</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">3982<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(fit_indices) <- list(model = names(models),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">3982<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dataset = names(datasets))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">3982<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_function <- function(fit_index) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> w <- which(fit_indices == fit_index, arr.ind = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_index <- w[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dataset_index <- w[2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- try(mkinfit(models[[model_index]], datasets[[dataset_index]], ...))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(res, "try-error")) res$mkinmod$name <- names(models)[model_index]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">793<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">3982<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_time <- system.time({</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">3982<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(cluster)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">2154<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> results <- parallel::mclapply(as.list(1:n.fits), fit_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">2154<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mc.cores = cores, mc.preschedule = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">1828<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">3798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attributes(results) <- attributes(fit_indices)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">3798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(results, "call") <- call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">3798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(results, "time") <- fit_time</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">3798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(results) <- "mmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">3798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(results)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Subsetting method for mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An \code{\link{mmkin} object}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param i Row index selecting the fits for specific models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param j Column index selecting the fits to specific datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ... Not used, only there to satisfy the generic method definition</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param drop If FALSE, the method always returns an mmkin object, otherwise</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' either a list of mkinfit objects or a single mkinfit object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object of class \code{\link{mmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname Extract.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Only use one core, to pass R CMD check --as-cran</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cores = 1, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits["FOMC", ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits[, "B"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits["SFO", "B"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' head(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This extracts an mkinfit object with lots of components</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits[["FOMC", "B"]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">`[.mmkin` <- function(x, i, j, ..., drop = FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">2760<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">2760<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x_sub <- x[i, j, drop = drop]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">2760<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!drop) class(x_sub) <- "mmkin"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">2760<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(x_sub)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print method for mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An [mmkin] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mmkin <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<mmkin> object\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Status of individual fits:\n\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">375<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(status(x))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.mmkin <- function(object, ..., evaluate = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- attr(object, "call")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments <- match.call(expand.dots = FALSE)$...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(update_arguments) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_in_call <- !is.na(match(names(update_arguments), names(call)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (a in names(update_arguments)[update_arguments_in_call]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">115<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[a]] <- update_arguments[[a]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_not_in_call <- !update_arguments_in_call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(any(update_arguments_not_in_call)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">193</td> + <td class="coverage">206<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- c(as.list(call), update_arguments[update_arguments_not_in_call])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">206<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- as.call(call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">195</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">197</td> + <td class="coverage">256<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(evaluate) eval(call, parent.frame())</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">198</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinpredict.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Produce predictions from a kinetic model using specific parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function produces a time series for all the observed variables in a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic model as specified by [mkinmod], using a specific set of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic parameters and initial values for the state variables.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @aliases mkinpredict mkinpredict.mkinmod mkinpredict.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x A kinetic model as produced by [mkinmod], or a kinetic fit as</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitted by [mkinfit]. In the latter case, the fitted parameters are used for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the prediction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param odeparms A numeric vector specifying the parameters used in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic model, which is generally defined as a set of ordinary differential</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' equations.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param odeini A numeric vector containing the initial values of the state</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables of the model. Note that the state variables can differ from the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed variables, for example in the case of the SFORB model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param outtimes A numeric vector specifying the time points for which model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' predictions should be generated.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param solution_type The method that should be used for producing the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' predictions. This should generally be "analytical" if there is only one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed variable, and usually "deSolve" in the case of several observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables. The third possibility "eigen" is fast in comparison to uncompiled</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ODE models, but not applicable to some models, e.g. using FOMC for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent compound.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method.ode The solution method passed via [mkinpredict] to [ode]] in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' case the solution type is "deSolve" and we are not using compiled code.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' When using compiled code, only lsoda is supported.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param use_compiled If set to \code{FALSE}, no compiled version of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mkinmod] model is used, even if is present.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param use_symbols If set to \code{TRUE} (default), symbol info present in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the [mkinmod] object is used if available for accessing compiled code</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param atol Absolute error tolerance, passed to the ode solver.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rtol Absolute error tolerance, passed to the ode solver.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param maxsteps Maximum number of steps, passed to the ode solver.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param map_output Boolean to specify if the output should list values for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the observed variables (default) or for all state variables (if set to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FALSE). Setting this to FALSE has no effect for analytical solutions,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as these always return mapped output.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param na_stop Should it be an error if [ode] returns NaN values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments passed to the ode solver in case such a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solver is used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A matrix with the numeric solution in wide format</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO <- mkinmod(degradinol = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Compare solution types</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "analytical")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve", use_compiled = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "eigen")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Compare integration methods to analytical solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "analytical")[21,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method = "lsoda", use_compiled = FALSE)[21,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method = "ode45", use_compiled = FALSE)[21,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method = "rk4", use_compiled = FALSE)[21,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # rk4 is not as precise here</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The number of output times used to make a lot of difference until the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # default for atol was adjusted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' seq(0, 20, by = 0.1))[201,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' seq(0, 20, by = 0.01))[2001,]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Comparison of the performance of solution types</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = list(type = "SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if(require(rbenchmark)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' benchmark(replications = 10, order = "relative", columns = c("test", "relative", "elapsed"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' eigen = mkinpredict(SFO_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "eigen")[201,],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deSolve_compiled = mkinpredict(SFO_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve")[201,],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deSolve = mkinpredict(SFO_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve", use_compiled = FALSE)[201,],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' analytical = mkinpredict(SFO_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "analytical", use_compiled = FALSE)[201,])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Predict from a fitted model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE, solution_type = "deSolve")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' head(mkinpredict(f))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinpredict <- function(x, odeparms, odeini, outtimes, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("mkinpredict", x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkinpredict</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinpredict.mkinmod <- function(x,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms = c(k_parent_sink = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini = c(parent = 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes = seq(0, 120, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "deSolve",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> use_compiled = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> use_symbols = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> map_output = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> na_stop = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Names of state variables and observed variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(x$diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- names(x$spec)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Order the inital values for state variables if they are named</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(names(odeini))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- odeini[mod_vars]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_obs <- matrix(NA, nrow = length(outtimes), ncol = 1 + length(obs_vars),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(as.character(outtimes), c("time", obs_vars)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_obs[, "time"] <- outtimes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_out_na <- 0 # to check if we get NA values with deSolve</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">47544878<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "analytical") {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # This is clumsy, as we wanted fast analytical predictions for mkinfit,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # which bypasses mkinpredict in the case of analytical solutions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pseudo_observed <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data.frame(name = rep(obs_vars, each = length(outtimes)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = rep(outtimes, length(obs_vars)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pseudo_observed$predicted <- x$deg_func(pseudo_observed, odeini, odeparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">2431585<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_obs[, obs_var] <- pseudo_observed[pseudo_observed$name == obs_var, "predicted"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We don't have solutions for unobserved state variables, the output of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # analytical solutions is always mapped to observed variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">1843695<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(out_obs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "eigen") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> evalparse <- function(string) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">392283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> eval(parse(text=string), as.list(c(odeparms, odeini)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> coefmat.num <- matrix(sapply(as.vector(x$coefmat), evalparse),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nrow = length(mod_vars))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> e <- eigen(coefmat.num)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c <- solve(e$vectors, odeini)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">165</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f.out <- function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">1085040<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> e$vectors %*% diag(exp(e$values * t), nrow=length(mod_vars)) %*% c</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> o <- matrix(mapply(f.out, outtimes),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nrow = length(mod_vars), ncol = length(outtimes))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- cbind(outtimes, t(o))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">97082<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(out) <- c("time", mod_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (solution_type == "deSolve") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">45604101<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$cf) & use_compiled[1] != FALSE) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$symbols) & use_symbols) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">1427314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lsoda_func <- x$symbols</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">44175921<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lsoda_func <- "diffs"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- deSolve::lsoda(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> y = odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">185</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> times = outtimes,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = lsoda_func,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> initfunc = "initpar",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dllname = x$dll_info[["name"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms = odeparms[x$parms], # Order matters when using compiled models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = atol,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rtol = rtol,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> maxsteps = maxsteps,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">195</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">45603235<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(out) <- c("time", mod_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkindiff <- function(t, state, parms) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time <- t</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in names(x$diffs))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffname <- paste("d", box, sep="_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs[diffname] <- with(as.list(c(time, state, parms)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> eval(parse(text=x$diffs[[box]])))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">145229<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(list(c(diffs)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">209</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out <- deSolve::ode(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> y = odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> times = outtimes,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = mkindiff,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms = odeparms,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">215</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method = method.ode,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> atol = atol,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rtol = rtol,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">866<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> maxsteps = maxsteps,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">45604101<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_out_na <- sum(is.na(out))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">45604101<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_out_na > 0 & na_stop) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">224</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("odeini:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">225</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(odeini)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">226</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("odeparms:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">227</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(odeparms)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">228</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("out:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">229</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(out)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">230</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Differential equations were not integrated for all output times because\n",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">231</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> n_out_na, " NaN values occurred in output from ode()")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (map_output) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Output transformation for models with unobserved compartments like SFORB</pre> + </td> + </tr> + <tr class="never"> + <td class="num">237</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # if not already mapped in analytical solution</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">238</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_out_na > 0 & !na_stop) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">239</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> available <- c(TRUE, rep(FALSE, length(outtimes) - 1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">240</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> available <- rep(TRUE, length(outtimes))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (var in names(x$map)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">244</td> + <td class="coverage">93237433<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if((length(x$map[[var]]) == 1)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">93235081<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_obs[available, var] <- out[available, var]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">2352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_obs[available, var] <- out[available, x$map[[var]][1]] +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">2352<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out[available, x$map[[var]][2]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">249</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">45701183<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(out_obs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">252</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">253</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(out) <- list(time = as.character(outtimes), c("time", mod_vars))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">254</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(out)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkinpredict</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinpredict.mkinfit <- function(x,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">261</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms = x$bparms.ode,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini = x$bparms.state,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">263</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes = seq(0, 120, by = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">264</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = "deSolve",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> use_compiled = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">266</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">267</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> map_output = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">268</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">269</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> mkinpredict(x$mkinmod, odeparms, odeini, outtimes, solution_type, use_compiled,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">270</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> method.ode, atol, rtol, map_output, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/anova.saem.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Anova method for saem.mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Generate an anova object. The method to calculate the BIC is that from the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' saemix package. As in other prominent anova methods, models are sorted by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' number of parameters, and the tests (if requested) are always relative to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the model on the previous line.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An [saem.mmkin] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ... further such objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method Method for likelihood calculation: "is" (importance sampling),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "lin" (linear approximation), or "gq" (Gaussian quadrature). Passed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to [saemix::logLik.SaemixObject]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param test Should a likelihood ratio test be performed? If TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the alternative models are tested against the first model. Should</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' only be done for nested models.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param model.names Optional character vector of model names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats anova logLik update pchisq terms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom methods is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom utils capture.output</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return an "anova" data frame; the traditional (S3) result of anova()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">anova.saem.mmkin <- function(object, ...,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method = c("is", "lin", "gq"), test = FALSE, model.names = NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # The following code is heavily inspired by anova.lmer in the lme4 package</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">26</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mCall <- match.call(expand.dots = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dots <- list(...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method <- match.arg(method)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> is_model <- sapply(dots, is, "saem.mmkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(is_model)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mods <- c(list(object), dots[is_model])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> successful <- sapply(mods, function(x) !inherits(x$so, "try-error"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(model.names))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">36</td> + <td class="coverage">284<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model.names <- vapply(as.list(mCall)[c(FALSE, TRUE, is_model)], deparse1, "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Sanitize model names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(model.names) != length(mods))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">40</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Model names vector and model list have different lengths")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(duplicated(model.names)))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">43</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Duplicate model names are not allowed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (max(nchar(model.names)) > 200) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">46</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Model names longer than 200 characters, assigning generic names")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">47</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> model.names <- paste0("MODEL",seq_along(model.names))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(mods) <- model.names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mods <- mods[successful]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Ensure same data, ignoring covariates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> same_data <- sapply(mods[-1], function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">1182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> identical(mods[[1]]$data[c("ds", "name", "time", "value")],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">1182<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x$data[c("ds", "name", "time", "value")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all(same_data)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">58</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop(sum(!same_data), " objects have not been fitted to the same data")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llks <- lapply(names(mods), function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">1700<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llk <- try(logLik(mods[[x]], method = method), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">1700<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(llk, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">64</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Could not obtain log likelihood with '", method, "' method for ", x)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">65</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> llk <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">1700<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(llk)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> available <- !sapply(llks, is.na)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llks <- llks[available]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mods <- mods[available]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Order models by increasing degrees of freedom:</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> npar <- vapply(llks, attr, FUN.VALUE=numeric(1), "df")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ii <- order(npar)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mods <- mods[ii]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llks <- llks[ii]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> npar <- npar[ii]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Describe data for the header, as in summary.saem.mmkin</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> header <- paste("Data:", nrow(object$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(object$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(object$data$ds)), "datasets\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Calculate statistics</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llk <- unlist(llks)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chisq <- 2 * pmax(0, c(NA, diff(llk)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dfChisq <- c(NA, diff(npar))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bic <- function(x, method) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">1700<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> BIC(x$so, method = method)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val <- data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> npar = npar,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> AIC = sapply(llks, AIC),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> BIC = sapply(mods, bic, method = method), # We use the saemix method here</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Lik = llk,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = names(mods), check.names = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (test) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> testval <- data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Chisq = chisq,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Df = dfChisq,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "Pr(>Chisq)" = ifelse(dfChisq == 0, NA,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pchisq(chisq, dfChisq, lower.tail = FALSE)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = names(mods), check.names = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">196<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val <- cbind(val, testval)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(val) <- c("anova", class(val))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">518<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> structure(val, heading = c(header))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">112</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Currently, no anova method is implemented for the case of a single saem.mmkin object")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/create_deg_func.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Create degradation functions for known analytical solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param spec List of model specifications as contained in mkinmod objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param use_of_ff Minimum or maximum use of formation fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Degradation function to be attached to mkinmod objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (require(rbenchmark))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' benchmark(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' replications = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' DFOP_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("DFOP", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' benchmark(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' replications = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">create_deg_func <- function(spec, use_of_ff = c("min", "max")) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_of_ff <- match.arg(use_of_ff)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> min_ff <- use_of_ff == "min"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- names(spec)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent <- obs_vars[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">36</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_type <- spec[[1]]$type</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> supported <- TRUE # This may be modified below</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text <- character(0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "SFO") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">5916<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (min_ff) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">599<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> targets <- c(spec[[1]]$to, if (spec[[1]]$sink) "sink" else NULL)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">599<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_parent <- paste(paste0("k_", parent, "_", targets), collapse = " + ")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">5317<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_parent <- paste0("k_", parent)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text[parent] <- paste0(parent_type, ".solution(t, odeini['", parent,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_type == "SFORB") "_free", "'], ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> switch(parent_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFO = k_parent,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> FOMC = "alpha, beta",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> IORE = paste0("k__iore_", parent, if (min_ff) "_sink" else "", ", N_", parent),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> DFOP = "k1, k2, g",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> SFORB = paste0("k_", parent, "_free_bound, k_", parent, "_bound_free, k_", parent, "_free", if (min_ff) "_sink" else ""),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> HS = "k1, k2, tb",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> logistic = "kmax, k0, r"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ")")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">3728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) >= 2) supported <- FALSE</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Except for the following cases:</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) == 2) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n1 <- obs_vars[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n2 <- obs_vars[2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n10 <- paste0("odeini['", parent, "']")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n20 <- paste0("odeini['", n2, "']")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # sfo_sfo</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$sink == FALSE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[2]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> is.null(spec[[2]]$to))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> supported <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- k_parent</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- paste0("k_", n2, if(min_ff) "_sink" else "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text[n2] <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "(((", k2, "-", k1, ")*", n20, "-", k1, "*", n10, ")*exp(-", k2, "*t)+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1, "*", n10, "*exp(-", k1, "*t))/(", k2, "-", k1, ")")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # sfo_f12_sfo</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_of_ff == "max",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$sink == TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[2]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> is.null(spec[[2]]$to))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> supported <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- k_parent</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- paste0("k_", n2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- paste0("f_", n1, "_to_", n2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text[n2] <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "(((", k2, "-", k1, ")*", n20, "-", f12, "*", k1, "*", n10, ")*exp(-", k2, "*t)+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">1129<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12, "*", k1, "*", n10, "*exp(-", k1, "*t))/(", k2, "-", k1, ")")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # sfo_k120_sfo</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_of_ff == "min",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$sink == TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[2]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> is.null(spec[[2]]$to))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> supported <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k12 <- paste0("k_", n1, "_", n2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k10 <- paste0("k_", n1, "_sink")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- paste0("k_", n2, "_sink")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text[n2] <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "(((", k2, "-", k12, "-", k10, ")*", n20, "-", k12, "*", n10, ")*exp(-", k2, "*t)+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">351<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k12, "*", n10, "*exp(-(", k_parent, ")*t))/(", k2, "-(", k_parent, "))")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # dfop_f12_sfo</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> use_of_ff == "max",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$sink == TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[1]]$type == "DFOP",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec[[2]]$type == "SFO",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">3036<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> is.null(spec[[2]]$to))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> supported <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f12 <- paste0("f_", n1, "_to_", n2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- paste0("k_", n2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> predicted_text[n2] <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "((", f12, "* g - ", f12, ") * k2 * ", n10, " * exp(- k2 * t))/(k2 - ", k2, ") - ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "((", f12, "* g) * k1 * ", n10, " * exp(- k1 * t))/(k1 - ", k2, ") + ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "(((k1 - ", k2, ") * k2 - ", k2, "* k1 + ", k2, "^2) * ", n20, "+",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "((", f12, "* k1 + (", f12, "*g - ", f12, ") * ", k2, ") * k2 - ", f12, " * g * ", k2, " * k1) * ", n10, ") * ",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">565<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "exp( - ", k2, " * t)/((k1 - ", k2, ") * k2 - ", k2, " * k1 + ", k2, "^2)")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">8117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (supported) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deg_func <- function(observed, odeini, odeparms) {}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_body <- paste0("{\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "predicted <- numeric(0)\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "with(as.list(odeparms), {\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">9961<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_body <- paste0(f_body,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">9961<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "t <- observed[observed$name == '", obs_var, "', 'time']\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">9961<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "predicted <<- c(predicted, ", predicted_text[obs_var], ")\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_body <- paste0(f_body,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "})\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "return(predicted)\n}\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> body(deg_func) <- parse(text = f_body)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">7175<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(deg_func)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">942<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/nlme.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Helper functions to create nlme models from mmkin row objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' These functions facilitate setting up a nonlinear mixed effects model for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' an mmkin row object. An mmkin row object is essentially a list of mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' objects that have been obtained by fitting the same model to a list of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' datasets. They are used internally by the [nlme.mmkin()] method.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An mmkin row object containing several fits of the same model to different datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @import nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso \code{\link{nlme.mmkin}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_SFO <- mkinmod(parent = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_1 <- mkinpredict(m_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 98), sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_2 <- mkinpredict(m_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.05),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 102), sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_3 <- mkinpredict(m_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.02),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 103), sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d1 <- add_err(d_SFO_1, function(value) 3, n = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d2 <- add_err(d_SFO_2, function(value) 2, n = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d3 <- add_err(d_SFO_3, function(value) 4, n = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds <- c(d1 = d1, d2 = d2, d3 = d3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin("SFO", ds, cores = 1, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mean_dp <- mean_degparms(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' grouped_data <- nlme_data(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nlme_f <- nlme_function(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # These assignments are necessary for these objects to be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # visible to nlme and augPred when evaluation is done by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # pkgdown to generate the html docs.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' assign("nlme_f", nlme_f, globalenv())</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' assign("grouped_data", grouped_data, globalenv())</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' data = grouped_data,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fixed = parent_0 + log_k_parent_sink ~ 1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' random = pdDiag(parent_0 + log_k_parent_sink ~ 1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' start = mean_dp)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(m_nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # augPred does not work on fits with more than one state</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # variable</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The procedure is greatly simplified by the nlme.mmkin function</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme <- nlme(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A function that can be used with nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nlme_function <- function(object) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">60</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkin_model <- object[[1]]$mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_names <- names(mean_degparms(object))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Inspired by https://stackoverflow.com/a/12983961/3805440</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and https://stackoverflow.com/a/26280789/3805440</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function_alist <- replicate(length(degparm_names) + 2, substitute())</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(model_function_alist) <- c("name", "time", degparm_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function_body <- quote({</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> arg_frame <- as.data.frame(as.list((environment())), stringsAsFactors = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_frame <- arg_frame[1:2]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_frame <- arg_frame[-(1:2)]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_unique <- unique(parm_frame)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_unique <- nrow(parms_unique)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> times_ds <- list()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names_ds <- list()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:n_unique) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> times_ds[[i]] <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> arg_frame[which(arg_frame[[3]] == parms_unique[i, 1]), "time"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names_ds[[i]] <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> arg_frame[which(arg_frame[[3]] == parms_unique[i, 1]), "name"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_list <- lapply(1:n_unique, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms_optim <- unlist(parms_unique[x, , drop = TRUE])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_fixed <- object[[1]]$bparms.fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_optim_parm_names <- grep('_0$', names(transparms_optim), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_optim <- transparms_optim[odeini_optim_parm_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed_parm_names <- grep('_0$', names(parms_fixed), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini_fixed <- parms_fixed[odeini_fixed_parm_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ode_transparms_optim_names <- setdiff(names(transparms_optim), odeini_optim_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = object[[1]]$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = object[[1]]$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_fixed_names <- setdiff(names(parms_fixed), odeini_fixed_parm_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms_fixed <- parms_fixed[odeparms_fixed_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms <- c(odeparms_optim, odeparms_fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_wide <- mkinpredict(mkin_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> odeparms = odeparms, odeini = odeini,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> solution_type = object[[1]]$solution_type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> outtimes = sort(unique(times_ds[[x]])))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_array <- out_wide[, -1, drop = FALSE]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(out_array) <- as.character(unique(times_ds[[x]]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_times <- as.character(times_ds[[x]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_names <- as.character(names_ds[[x]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_values <- mapply(function(times, names) out_array[times, names],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> out_times, out_names)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">2342789<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(as.numeric(out_values))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- unlist(res_list)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">252739<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_function <- as.function(c(model_function_alist, model_function_body))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">1168<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(model_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom rlang !!!</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A \code{\link{groupedData}} object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nlme_data <- function(object) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">132</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_names <- colnames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds_list) <- ds_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_nlme <- vctrs::vec_rbind(!!!ds_list, .names_to = "ds")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_nlme$variable <- as.character(ds_nlme$variable)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_nlme$ds <- ordered(ds_nlme$ds, levels = unique(ds_nlme$ds))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_nlme_renamed <- data.frame(ds = ds_nlme$ds, name = ds_nlme$variable,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = ds_nlme$time, value = ds_nlme$observed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stringsAsFactors = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_nlme_grouped <- groupedData(value ~ time | ds, ds_nlme_renamed, order.groups = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">5677<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ds_nlme_grouped)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/transform_odeparms.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Functions to transform and backtransform kinetic parameters for fitting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The transformations are intended to map parameters that should only take on</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' restricted values to the full scale of real numbers. For kinetic rate</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' constants and other parameters that can only take on positive values, a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' simple log transformation is used. For compositional parameters, such as the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' formations fractions that should always sum up to 1 and can not be negative,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the [ilr] transformation is used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The transformation of sets of formation fractions is fragile, as it supposes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the same ordering of the components in forward and backward transformation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This is no problem for the internal use in [mkinfit].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param parms Parameters of kinetic models as used in the differential</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' equations.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transparms Transformed parameters of kinetic models as used in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitting procedure.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param mkinmod The kinetic model of class [mkinmod], containing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the names of the model variables that are needed for grouping the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' formation fractions before [ilr] transformation, the parameter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names and the information if the pathway to sink is included in the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transform_rates Boolean specifying if kinetic rate constants should</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be transformed in the model specification used in the fitting for better</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compliance with the assumption of normal distribution of the estimator. If</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' TRUE, also alpha and beta parameters of the FOMC model are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' log-transformed, as well as k1 and k2 rate constants for the DFOP and HS</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' models and the break point tb of the HS model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transform_fractions Boolean specifying if formation fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' constants should be transformed in the model specification used in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitting for better compliance with the assumption of normal distribution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the estimator. The default (TRUE) is to do transformations.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The g parameter of the DFOP model is also seen as a fraction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If a single fraction is transformed (g parameter of DFOP or only a single</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' target variable e.g. a single metabolite plus a pathway to sink), a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' logistic transformation is used [stats::qlogis()]. In other cases, i.e. if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' two or more formation fractions need to be transformed whose sum cannot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' exceed one, the [ilr] transformation is used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A vector of transformed or backtransformed parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats plogis qlogis</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = list(type = "SFO", to = "m1", sink = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = list(type = "SFO"), use_of_ff = "min")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Fit the model to the FOCUS example dataset D using defaults</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.s <- summary(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Transformed and backtransformed parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.s$par, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.s$bpar, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Compare to the version without transforming rate parameters (does not work</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # with analytical solution, we get NA values for m1 in predictions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' solution_type = "deSolve", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.2.s <- summary(fit.2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.2.s$par, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.2.s$bpar, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' initials <- fit$start$value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(initials) <- rownames(fit$start)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformed <- fit$start_transformed$value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(transformed) <- rownames(fit$start_transformed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transform_odeparms(initials, SFO_SFO)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' backtransform_odeparms(transformed, SFO_SFO)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The case of formation fractions (this is now the default)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO.ff <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = list(type = "SFO", to = "m1", sink = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = list(type = "SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.ff.s <- summary(fit.ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.ff.s$par, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.ff.s$bpar, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' initials <- c("f_parent_to_m1" = 0.5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformed <- transform_odeparms(initials, SFO_SFO.ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' backtransform_odeparms(transformed, SFO_SFO.ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # And without sink</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO.ff.2 <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = list(type = "SFO", to = "m1", sink = FALSE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = list(type = "SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.ff.2.s <- summary(fit.ff.2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.ff.2.s$par, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(fit.ff.2.s$bpar, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export transform_odeparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">transform_odeparms <- function(parms, mkinmod,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = TRUE, transform_fractions = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We need the model specification for the names of the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # variables and the information on the sink</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec = mkinmod$spec</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set up container for transformed parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms <- numeric(0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not transform initial values for state variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.optim <- parms[grep("_0$", names(parms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[names(state.ini.optim)] <- state.ini.optim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Log transformation for rate constants if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k <- parms[grep("^k_", names(parms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k__iore <- parms[grep("^k__iore_", names(parms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k <- c(k, k__iore)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(k) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">120</td> + <td class="coverage">15485<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(transform_rates) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">14379<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[paste0("log_", names(k))] <- log(k)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">1106<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> } else transparms[names(k)] <- k</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not transform exponents in IORE models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">126</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N <- parms[grep("^N", names(parms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">127</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[names(N)] <- N</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Go through state variables and transform formation fractions if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars = names(spec)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">41283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f <- parms[grep(paste("^f", box, sep = "_"), names(parms))]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">41283<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(f) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">6522<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(transform_fractions) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">5910<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (spec[[box]]$sink) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">5908<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(f) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">5894<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f_name <- paste("f", box, "qlogis", sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">5894<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[trans_f_name] <- qlogis(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">14<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f <- ilr(c(f, 1 - sum(f)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">14<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f_names <- paste("f", box, "ilr", 1:length(trans_f), sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">14<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[trans_f_names] <- trans_f</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(f) > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f <- ilr(f)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f_names <- paste("f", box, "ilr", 1:length(trans_f), sep = "_")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[trans_f_names] <- trans_f</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">612<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[names(f)] <- f</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform also FOMC parameters alpha and beta, DFOP and HS rates k1 and k2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and HS parameter tb as well as logistic model parameters kmax, k0 and r if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # transformation of rates is requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in c("alpha", "beta", "k1", "k2", "tb", "kmax", "k0", "r")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">204696<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(parms[pname])) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">6006<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transform_rates) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">6006<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[paste0("log_", pname)] <- log(parms[pname])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">166</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> transparms[pname] <- parms[pname]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # DFOP parameter g is treated as a fraction</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(parms["g"])) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">1978<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- parms["g"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">1978<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transform_fractions) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">1978<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transparms["g_qlogis"] <- qlogis(g)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">177</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> transparms["g"] <- g</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">25587<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(transparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">183</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname transform_odeparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export backtransform_odeparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">backtransform_odeparms <- function(transparms, mkinmod,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We need the model specification for the names of the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # variables and the information on the sink</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec = mkinmod$spec</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set up container for backtransformed parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms <- numeric(0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not transform initial values for state variables</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.ini.optim <- transparms[grep("_0$", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[names(state.ini.optim)] <- state.ini.optim</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Exponential transformation for rate constants</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(transform_rates) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">203</td> + <td class="coverage">49140623<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_k <- transparms[grep("^log_k_", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">49140623<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_k__iore <- transparms[grep("^log_k__iore_", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">49140623<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_k = c(trans_k, trans_k__iore)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">49140623<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(trans_k) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">47598103<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_names <- gsub("^log_k", "k", names(trans_k))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">47598103<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[k_names] <- exp(trans_k)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">209</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">73591<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_k <- transparms[grep("^k_", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">73591<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[names(trans_k)] <- trans_k</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">213</td> + <td class="coverage">73591<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_k__iore <- transparms[grep("^k__iore_", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">73591<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[names(trans_k__iore)] <- trans_k__iore</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">217</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Do not transform exponents in IORE models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N <- transparms[grep("^N", names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[names(N)] <- N</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Go through state variables and apply inverse transformations to formation fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars = names(spec)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the names as used in the model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">97593385<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names = grep(paste("^f", box, sep = "_"), mkinmod$parms, value = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get the formation fraction parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">97593385<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> trans_f = transparms[grep(paste("^f", box, sep = "_"), names(transparms))]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">97593385<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(trans_f) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">46632823<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(transform_fractions) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">46588453<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(grepl("qlogis", names(trans_f)))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">232</td> + <td class="coverage">46059152<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_tmp <- plogis(trans_f)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">46059152<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[f_names] <- f_tmp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_tmp <- invilr(trans_f)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (spec[[box]]$sink) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">528393<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[f_names] <- f_tmp[1:length(f_tmp)-1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">908<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[f_names] <- f_tmp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">240</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">241</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">242</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">44370<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[names(trans_f)] <- trans_f</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">245</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">246</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">247</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">248</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform parameters also for FOMC, DFOP, HS and logistic models</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in c("alpha", "beta", "k1", "k2", "tb", "kmax", "k0", "r")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">250</td> + <td class="coverage">393713712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transform_rates) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">393124984<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pname_trans = paste0("log_", pname)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">393124984<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(transparms[pname_trans])) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">4306142<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms[pname] <- exp(transparms[pname_trans])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">255</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">256</td> + <td class="coverage">588728<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(transparms[pname])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">257</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> parms[pname] <- transparms[pname]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">261</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # DFOP parameter g is now transformed using qlogis</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(transparms["g_qlogis"])) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">2034008<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g_qlogis <- transparms["g_qlogis"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">265</td> + <td class="coverage">2034008<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms["g"] <- plogis(g_qlogis)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">266</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">267</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # In earlier times we used ilr for g, so we keep this around</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">268</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(transparms["g_ilr"])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">269</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> g_ilr <- transparms["g_ilr"]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">270</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> parms["g"] <- invilr(g_ilr)[1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(transparms["g"])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">273</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> parms["g"] <- transparms["g"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">274</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">275</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">276</td> + <td class="coverage">49214214<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(parms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">277</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">278</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># vim: set ts=2 sw=2 expandtab:</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/hierarchical_kinetics.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Hierarchical kinetics template</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' R markdown format for setting up hierarchical kinetics based on a template</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' provided with the mkin package. This format is based on [rmarkdown::pdf_document].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Chunk options are adapted. Echoing R code from code chunks and caching are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' turned on per default. character for prepending output from code chunks is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set to the empty string, code tidying is off, figure alignment defaults to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' centering, and positioning of figures is set to "H", which means that</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' figures will not move around in the document, but stay where the user</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' includes them.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The latter feature (positioning the figures with "H") depends on the LaTeX</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' package 'float'. In addition, the LaTeX package 'listing' is used in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' template for showing model fit summaries in the Appendix. This means that</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the LaTeX packages 'float' and 'listing' need to be installed in the TeX</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' distribution used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' On Windows, the easiest way to achieve this (if no TeX distribution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is present before) is to install the 'tinytex' R package, to run</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'tinytex::install_tinytex()' to get the basic tiny Tex distribution,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inheritParams rmarkdown::pdf_document</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ... Arguments to \code{rmarkdown::pdf_document}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return R Markdown output format to pass to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link[rmarkdown:render]{render}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(rmarkdown)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The following is now commented out after the relase of v1.2.3 for the generation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # of online docs, as the command creates a directory and opens an editor</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">hierarchical_kinetics <- function(..., keep_tex = FALSE) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">41</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (getRversion() < "4.1.0")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">42</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("You need R with version > 4.1.0 to compile this document")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">44</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!requireNamespace("knitr")) stop("Please install the knitr package to use this template")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">45</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!requireNamespace("rmarkdown")) stop("Please install the rmarkdown package to use this template")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">46</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> knitr::opts_chunk$set(cache = TRUE, comment = "", tidy = FALSE, echo = TRUE)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">47</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> knitr::opts_chunk$set(fig.align = "center", fig.pos = "H")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">48</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> options(knitr.kable.NA = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">50</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> fmt <- rmarkdown::pdf_document(...,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">51</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> keep_tex = keep_tex,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">52</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> toc = TRUE,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">53</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> toc_depth = 3,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">54</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> includes = rmarkdown::includes(in_header = "header.tex"),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">55</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> extra_dependencies = c("float", "listing", "framed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">58</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(fmt)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/nlme.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># Code inspired by nlme::nlme.nlsList and R/nlme_fit.R from nlmixr</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># We need to assign the degradation function created in nlme.mmkin to an</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># environment that is always accessible, also e.g. when evaluation is done by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># testthat or pkgdown. Therefore parent.frame() is not good enough. The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># following environment will be in the mkin namespace.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">.nlme_env <- new.env(parent = emptyenv())</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nlme::nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Retrieve a degradation function from the mmkin namespace</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom utils getFromNamespace</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A function that was likely previously assigned from within</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nlme.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">get_deg_func <- function() {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">19</td> + <td class="coverage">217279<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(get("deg_func", getFromNamespace(".nlme_env", "mkin")))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Create an nlme model for an mmkin row object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This functions sets up a nonlinear mixed effects model for an mmkin row</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' object. An mmkin row object is essentially a list of mkinfit objects that</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' have been obtained by fitting the same model to a list of datasets.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Note that the convergence of the nlme algorithms depends on the quality</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the data. In degradation kinetics, we often only have few datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (e.g. data for few soils) and complicated degradation models, which may</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' make it impossible to obtain convergence with nlme.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param model An [mmkin] row object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data Ignored, data are taken from the mmkin model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fixed Ignored, all degradation parameters fitted in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mmkin model are used as fixed parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param random If not specified, no correlations between random effects are</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set up for the optimised degradation model parameters. This is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' achieved by using the [nlme::pdDiag] method.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param groups See the documentation of nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param start If not specified, mean values of the fitted degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters taken from the mmkin object are used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param correlation See the documentation of nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param weights passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param subset passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param na.action passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param naPattern passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param control passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose passed to nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats na.fail as.formula</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Upon success, a fitted 'nlme.mmkin' object, which is an nlme object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' with additional elements. It also inherits from 'mixed.mmkin'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note As the object inherits from [nlme::nlme], there is a wealth of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' methods that will automatically work on 'nlme.mmkin' objects, such as</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [nlme::intervals()], [nlme::anova.lme()] and [nlme::coef.lme()].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [nlme_function()], [plot.mixed.mmkin], [summary.nlme.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds <- lapply(experimental_data_for_UBA_2019[6:10],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(x) subset(x$data[c("name", "time", "value")], name == "parent"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_sfo <- nlme(f["SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_dfop <- nlme(f["DFOP", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_nlme_sfo, f_nlme_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_nlme_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlme_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(f_nlme_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' function(x) x$data[c("name", "time", "value")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"), use_of_ff = "min", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A1 = mkinsub("SFO"), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_2 <- mmkin(list("SFO-SFO" = m_sfo_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "SFO-SFO-ff" = m_sfo_sfo_ff,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "DFOP-SFO" = m_dfop_sfo),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_2, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_sfo_sfo <- nlme(f_2["SFO-SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlme_sfo_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # With formation fractions this does not coverge with defaults</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #plot(f_nlme_sfo_sfo_ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # For the following, we need to increase pnlsMaxIter and the tolerance</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # to get convergence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' control = list(pnlsMaxIter = 120, tolerance = 5e-4))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_nlme_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(f_nlme_sfo_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(f_nlme_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (length(findFunction("varConstProp")) > 0) { # tc error model for nlme available</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Attempts to fit metabolite kinetics with the tc error model are possible,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # but need tweeking of control values and sometimes do not converge</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_tc <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_sfo_tc <- nlme(f_tc["SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_dfop_tc <- nlme(f_tc["DFOP", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_nlme_dfop_tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_2_obs <- update(f_2, error_model = "obs")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_nlme_sfo_sfo_obs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' control = list(pnlsMaxIter = 120, tolerance = 5e-4))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_2_tc <- update(f_2, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nlme.mmkin <- function(model, data = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed = lapply(as.list(names(mean_degparms(model))),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> function(el) eval(parse(text = paste(el, 1, sep = "~")))),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> random = pdDiag(fixed),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> groups,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> start = mean_degparms(model, random = TRUE, test_log_parms = TRUE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> correlation = NULL, weights = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> subset, method = c("ML", "REML"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> na.action = na.fail, naPattern,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> control = list(), verbose= FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">142</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(model) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall <- as.list(match.call())[-1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Warn in case arguments were used that are overriden</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(!is.na(match(names(thisCall),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> c("data"))))) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">149</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("'nlme.mmkin' will redefine 'data'")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get native symbol info for speed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (model[[1]]$solution_type == "deSolve" & !is.null(model[[1]]$mkinmod$cf)) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # The mkinmod stored in the first fit will be used by nlme</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model[[1]]$mkinmod$symbols <- deSolve::checkDLL(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">156</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dllname = model[[1]]$mkinmod$dll_info[["name"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> func = "diffs", initfunc = "initpar",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> jacfunc = NULL, nout = 0, outnames = NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deg_func <- nlme_function(model)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> assign("deg_func", deg_func, getFromNamespace(".nlme_env", "mkin"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # For the formula, get the degradation function from the mkin namespace</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> this_model_text <- paste0("value ~ mkin::get_deg_func()(",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(names(formals(deg_func)), collapse = ", "), ")")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> this_model <- as.formula(this_model_text)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["model"]] <- this_model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["data"]] <- nlme_data(model)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["start"]] <- start</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["fixed"]] <- fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["random"]] <- random</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> error_model <- model[[1]]$err_mod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (missing(weights)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["weights"]] <- switch(error_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = NULL,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">185</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = varIdent(form = ~ 1 | name),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = varConstProp())</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma <- switch(error_model,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = 1,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">189</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> NULL)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> control <- thisCall[["control"]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">193</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (error_model == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">928<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> control$sigma = 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">928<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> thisCall[["control"]] <- control</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_time <- system.time(val <- do.call("nlme.formula", thisCall))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$time <- fit_time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$mkinmod <- model[[1]]$mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Don't return addresses that will become invalid</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">203</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$mkinmod$symbols <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">204</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$data <- thisCall[["data"]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$mmkin <- model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">824<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.list(start)) val$mean_dp_start <- start$fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">189<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else val$mean_dp_start <- start</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$transform_rates <- model[[1]]$transform_rates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$transform_fractions <- model[[1]]$transform_fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$solution_type <- model[[1]]$solution_type</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$err_mode <- error_model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$bparms.optim <- backtransform_odeparms(val$coefficients$fixed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">215</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">216</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_rates = val$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform_fractions = val$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$bparms.fixed <- model[[1]]$bparms.fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">220</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$date.fit <- date()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$nlmeversion <- as.character(utils::packageVersion("nlme"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$mkinversion <- as.character(utils::packageVersion("mkin"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val$Rversion <- paste(R.version$major, R.version$minor, sep=".")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(val) <- c("nlme.mmkin", "mixed.mmkin", "nlme", "lme")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">1013<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(val)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">228</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">229</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname nlme.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An nlme.mmkin object to print</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.nlme.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat( "Kinetic nonlinear mixed-effects model fit by " )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat( if(x$method == "REML") "REML\n" else "maximum likelihood\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStructural model:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> diffs <- x$mmkin[[1]]$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">238</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(nrow(x$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$ds)), "datasets\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nLog-", if(x$method == "REML") "restricted-" else "",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">244</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "likelihood: ", format(x$logLik, digits = digits), "\n", sep = "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixF <- x$call$fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">246</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFixed effects:\n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">247</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deparse(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(inherits(fixF, "formula") || is.call(fixF) || is.name(fixF))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> x$call$fixed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">250</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> else</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">251</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lapply(fixF, function(el) as.name(deparse(el)))), "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(fixef(x), digits = digits, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">254</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(summary(x$modelStruct), sigma = x$sigma, digits = digits, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">255</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">256</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">257</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">258</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">259</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname nlme.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An nlme.mmkin object to update</pre> + </td> + </tr> + <tr class="never"> + <td class="num">261</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ... Update specifications passed to update.nlme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">262</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.nlme.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">85<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- NextMethod()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">85<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res$mmkin <- object$mmkin</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">265</td> + <td class="coverage">85<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(res) <- c("nlme.mmkin", "nlme", "lme")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">85<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">267</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinresplot.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("variable", "residual"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to plot residuals stored in an mkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function plots the residuals for the specified subset of the observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variables from an mkinfit object. A combined plot of the fitted model and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the residuals can be obtained using \code{\link{plot.mkinfit}} using the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' argument \code{show_residuals = TRUE}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats residuals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A fit represented in an \code{\link{mkinfit}} object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param obs_vars A character vector of names of the observed variables for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' which residuals should be plotted. Defaults to all observed variables in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlim plot range in x direction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param xlab Label for the x axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param standardized Should the residuals be standardized by dividing by the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' standard deviation given by the error model of the fit?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ylab Label for the y axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param maxabs Maximum absolute value of the residuals. This is used for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' scaling of the y axis and defaults to "auto".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param legend Should a legend be plotted?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lpos Where should the legend be placed? Default is "topright". Will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be passed on to \code{\link{legend}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param col_obs Colors for the observed variables.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param pch_obs Symbols to be used for the observed variables.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param frame Should a frame be drawn around the plots?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots further arguments passed to \code{\link{plot}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Nothing is returned by this function, as it is called for its side</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' effect, namely to produce a plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke and Katrin Lindenberger</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso \code{\link{mkinplot}}, for a way to plot the data and the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lines of the mkinfit object, and \code{\link{plot_res}} for a function</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' combining the plot of the fit and the residual plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinresplot(fit, "m1")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinresplot <- function (object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars = names(object$mkinmod$map),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = c(0, 1.1 * max(object$data$time)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "Time", ylab = ifelse(standardized, "Standardized residual", "Residual"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> maxabs = "auto", legend = TRUE, lpos = "topright",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> col_obs = "auto", pch_obs = "auto",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> frame = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars_all <- as.character(unique(object$data$variable))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) > 0){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- intersect(obs_vars_all, obs_vars)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">56</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> } else obs_vars <- obs_vars_all</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (standardized) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">59</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> res_col <- "standardized"</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">60</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object$data[[res_col]] <- residuals(object, standardized = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_col <- "residual"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- subset(object$data, variable %in% obs_vars)[res_col]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (maxabs == "auto") maxabs = max(abs(res), na.rm = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set colors and symbols</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (col_obs[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> col_obs <- 1:length(obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (pch_obs[1] == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pch_obs <- 1:length(obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(col_obs) <- names(pch_obs) <- obs_vars</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(0, type = "n", frame = frame,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = xlab, ylab = ylab,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = xlim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = c(-1.2 * maxabs, 1.2 * maxabs), ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for(obs_var in obs_vars){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">1298<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> residuals_plot <- subset(object$data, variable == obs_var, c("time", res_col))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">1298<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(h = 0, lty = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">1228<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (legend == TRUE) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">91</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> legend(lpos, inset = c(0.05, 0.05), legend = obs_vars,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">92</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> col = col_obs[obs_vars], pch = pch_obs[obs_vars])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/plot.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot model fits (observed and fitted) and the residuals for a row or column</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of an mmkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' When x is a row selected from an mmkin object (\code{\link{[.mmkin}}), the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' same model fitted for at least one dataset is shown. When it is a column,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the fit of at least one model to the same dataset is shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' If the current plot device is a \code{\link[tikzDevice]{tikz}} device, then</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' latex is being used for the formatting of the chi2 error level.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An object of class \code{\link{mmkin}}, with either one row or one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' column.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param main The main title placed on the outer margin of the plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param legends An index for the fits for which legends should be shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param resplot Should the residuals plotted against time, using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinresplot}}, or as squared residuals against predicted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' values, with the error model, using \code{\link{mkinerrplot}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ylab Label for the y axis.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param standardized Should the residuals be standardized? This option</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is passed to \code{\link{mkinresplot}}, it only takes effect if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' `resplot = "time"`.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param show_errmin Should the chi2 error level be shown on top of the plots</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to the left?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param errmin_var The variable for which the FOCUS chi2 error value should</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param errmin_digits The number of significant digits for rounding the FOCUS</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' chi2 error percentage.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cex Passed to the plot functions and \code{\link{mtext}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rel.height.middle The relative height of the middle plot, if more</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' than two rows of plots are shown.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ymax Maximum y axis value for \code{\link{plot.mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinresplot}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Only use one core not to offend CRAN checks</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(c("FOMC", "HS"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cores = 1, quiet = TRUE, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits[, "FOCUS C"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits["FOMC", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits["FOMC", ], show_errmin = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # height should be smaller than the plot width (this is not possible for the html pages</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # generated by pkgdown, as far as I know).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Show the error models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(fits["FOMC", ], resplot = "errmod")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">plot.mmkin <- function(x, main = "auto", legends = 1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> resplot = c("time", "errmod"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ylab = "Residue",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> standardized = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> show_errmin = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin_var = "All data", errmin_digits = 3,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cex = 0.7, rel.height.middle = 0.9,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ymax = "auto", ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.m <- nrow(x)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.d <- ncol(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> resplot <- match.arg(resplot)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We can handle either a row (different models, same dataset)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # or a column (same model, different datasets)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">77</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.m > 1 & n.d > 1) stop("Please select fits either for one model or for one dataset")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">78</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.m == 1 & n.d == 1) loop_over = "none"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">246<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.m > 1) loop_over <- "models"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.d > 1) loop_over <- "datasets"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.fits <- length(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set the main plot titles from the names of the models or the datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Will be integer indexes if no other names are present in the mmkin object</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (main == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> main = switch(loop_over,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> none = paste(rownames(x), colnames(x)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> models = colnames(x),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> datasets = rownames(x))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set relative plot heights, so the first and the last plot are the norm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # and the middle plots (if n.fits >2) are smaller by rel.height.middle</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rel.heights <- if (n.fits > 2) c(1, rep(rel.height.middle, n.fits - 2), 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else rep(1, n.fits)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(cex = cex)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i.fit in 1:n.fits) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for top row of plots when we have more than one row</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Reduce bottom margin by 2.1 - hides x axis legend</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (i.fit == 1 & n.fits > 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3.0, 4.1, 4.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for middle rows of plots, if any</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (i.fit > 1 & i.fit < n.fits) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Reduce top margin by 2 after the first plot as we have no main title,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # reduced plot height, therefore we need rel.height.middle in the layout</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(3.0, 4.1, 2.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Margins for bottom row of plots when we have more than one row</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (i.fit == n.fits & n.fits > 1) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Restore bottom margin for last plot to show x axis legend</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">316<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(5.1, 4.1, 2.1, 2.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit <- x[[i.fit]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ymax == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> plot(fit, legend = legends == i.fit, ylab = ylab, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">125</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> plot(fit, legend = legends == i.fit, ylim = c(0, ymax), ylab = ylab, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">128</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> title(main, outer = TRUE, line = -2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_name <- switch(loop_over,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> models = rownames(x)[i.fit],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> datasets = colnames(x)[i.fit],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> none = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (show_errmin) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Use LateX if the current plotting device is tikz</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (names(dev.cur()) == "tikz output") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">140</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_text <- paste0(fit_name, " $\\chi^2$ error level = ", chi2, "\\%")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_perc <- paste0(chi2, "%")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> chi2_text <- bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2_perc))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mtext(chi2_text, cex = cex, line = 0.4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">147</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> mtext(fit_name, cex = cex, line = 0.4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (resplot == "time") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mkinresplot(fit, legend = FALSE, standardized = standardized, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">153</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> mkinerrplot(fit, legend = FALSE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">948<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/summary.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Summary method for class "mmkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Shows status information on the [mkinfit] objects contained in the object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and gives an overview of ill-defined parameters calculated by [illparms].</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object an object of class [mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x an object of class \code{summary.mmkin}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param conf.level confidence level for testing parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots optional arguments passed to methods like \code{print}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fits <- mmkin(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c("SFO", "FOMC"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list("FOCUS A" = FOCUS_2006_A,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "FOCUS C" = FOCUS_2006_C),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE, cores = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(fits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">summary.mmkin <- function(object, conf.level = 0.95, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">23</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ans <- list(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod = object[[1, 1]]$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = attr(object, "time"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">26</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> illparms = illparms(object),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> status = status(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(ans) <- c("summary.mmkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ans)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.summary.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">37</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$err_mod)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Error model: ")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(switch(x$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "Constant variance",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = "Variance unique to each observed variable",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = "Two-component variance function"), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Fitted in", x$time[["elapsed"]], "s\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStatus:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$status)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x$illparms != "")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nIll-defined parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$illparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/read_spreadsheet.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Read datasets and relevant meta information from a spreadsheet file</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function imports one dataset from each sheet of a spreadsheet file.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' These sheets are selected based on the contents of a sheet 'Datasets', with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a column called 'Dataset Number', containing numbers identifying the dataset</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sheets to be read in. In the second column there must be a grouping</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variable, which will often be named 'Soil'. Optionally, time normalization</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' factors can be given in columns named 'Temperature' and 'Moisture'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The first row read after the header read in from this sheet is assumed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to contain name and acronym of the parent compound.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The dataset sheets should be named using the dataset numbers read in from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the 'Datasets' sheet, i.e. '1', '2', ... . In each dataset sheet, the name</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the observed variable (e.g. the acronym of the parent compound or</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' one of its transformation products) should be in the first column,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the time values should be in the second colum, and the observed value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in the third column.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' In case relevant covariate data are available, they should be given</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in a sheet 'Covariates', containing one line for each value of the grouping</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variable specified in 'Datasets'. These values should be in the first</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' column and the column must have the same name as the second column in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'Datasets'. Covariates will be read in from columns four and higher.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Their names should preferably not contain special characters like spaces,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' so they can be easily used for specifying covariate models.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A similar data structure is defined as the R6 class [mkindsg], but</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is probably more complicated to use.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param path Absolute or relative path to the spreadsheet file</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param valid_datasets Optional numeric index of the valid datasets, default is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to use all datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param parent_only Should only the parent data be used?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param normalize Should the time scale be normalized using temperature</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and moisture normalisation factors in the sheet 'Datasets'?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">read_spreadsheet <- function(path, valid_datasets = "all",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_only = FALSE, normalize = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!requireNamespace("readxl", quietly = TRUE))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">43</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please install the readxl package to use this function")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Read the compound table</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> compounds <- readxl::read_excel(path, sheet = "Compounds")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent <- compounds[1, ]$Acronym</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Read in meta information</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_meta <- readxl::read_excel(path, sheet = "Datasets")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_meta["Dataset Number"] <- as.character(ds_meta[["Dataset Number"]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Select valid datasets</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">54</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (valid_datasets[1] == "all") valid_datasets <- 1:nrow(ds_meta)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_numbers_valid <- ds_meta[valid_datasets, ]$`Dataset Number`</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> grouping_factor <- names(ds_meta[2]) # Often "Soil"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Read in valid datasets</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_raw <- lapply(ds_numbers_valid,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(dsn) readxl::read_excel(path, sheet = as.character(dsn)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Make data frames compatible with mmkin</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_tmp <- lapply(ds_raw, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_ret <- x[1:3] |></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rlang::set_names(c("name", "time", "value")) |></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform(value = as.numeric(value))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds_tmp) <- ds_numbers_valid</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Normalize with temperature and moisture correction factors</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (normalize) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_norm <- lapply(ds_numbers_valid, function(ds_number) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_corr <- as.numeric(ds_meta[ds_number, c("Temperature", "Moisture")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_corr <- ds_tmp[[ds_number]] |></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transform(time = time * f_corr[1] * f_corr[2])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">1287<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ds_corr)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">79</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ds_norm <- ds_tmp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds_norm) <- ds_numbers_valid</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Select parent data only if requested</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (parent_only) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">85</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ds_norm <- lapply(ds_norm, function(x) subset(x, name == parent))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">86</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> compounds <- compounds[1, ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Create a single long table to combine datasets with the same group name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_all <- vctrs::vec_rbind(!!!ds_norm, .names_to = "Dataset Number")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds_all_group <- merge(ds_all, ds_meta[c("Dataset Number", grouping_factor)])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> groups <- unique(ds_meta[valid_datasets, ][[grouping_factor]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ds <- lapply(groups, function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">819<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret <- ds_all_group[ds_all_group[[grouping_factor]] == x, ]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">819<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret[c("name", "time", "value")]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(ds) <- groups</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get covariates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates_raw <- readxl::read_excel(path, sheet = "Covariates")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates <- as.data.frame(covariates_raw[4:ncol(covariates_raw)])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nocov <- setdiff(groups, covariates_raw[[1]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(nocov) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">106</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("Did not find covariate data for ", paste(nocov, collapse = ", "))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">107</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> message("Not returning covariate data")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">108</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> attr(ds, "covariates") <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(covariates) <- covariates_raw[[1]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates <- covariates[which(colnames(covariates) != "Remarks")]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Attach covariate data if available</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(ds, "covariates") <- covariates[groups, , drop = FALSE]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Attach the compound list to support automatic model building</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(ds, "compounds") <- as.data.frame(compounds)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ds)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/CAKE_export.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Export a list of datasets format to a CAKE study file</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' In addition to the datasets, the pathways in the degradation model can be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' specified as well.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ds A named list of datasets in long format as compatible with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param map A character vector with CAKE compartment names (Parent, A1, ...),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' named with the names used in the list of datasets.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param links An optional character vector of target compartments, named with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the names of the source compartments. In order to make this easier, the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names are used as in the datasets supplied.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param filename Where to write the result. Should end in .csf in order to be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compatible with CAKE.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param path An optional path to the output file.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param overwrite If TRUE, existing files are overwritten.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param study The name of the study.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param description An optional description.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param time_unit The time unit for the residue data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param res_unit The unit used for the residues.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param comment An optional comment.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param date The date of file creation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param optimiser Can be OLS or IRLS.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom utils write.table</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The function is called for its side effect.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">CAKE_export <- function(ds, map = c(parent = "Parent"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> links = NA,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> filename = "CAKE_export.csf", path = ".", overwrite = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> study = "Degradinol aerobic soil degradation",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> description = "",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> time_unit = "days",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> res_unit = "% AR",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> comment = "",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> date = Sys.Date(),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> optimiser = "IRLS")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> file <- file.path(path, filename)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (file.exists(file) & !overwrite) stop(file, " already exists, stopping")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> csf <- file(file, encoding = "latin1", open = "w+")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(close(csf))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> CAKE_compartments = c("Parent", "A1", "A2", "A3", "B1", "B2", "C1")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!all(map %in% CAKE_compartments)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("The elements of map have to be CAKE compartment names")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add <- function(x) cat(paste0(x, "\r\n"), file = csf, append = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add0 <- function(x) cat(x, file = csf, append = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("[FileInfo]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("CAKE-Version: 3.4 (Release)")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("Name:", study))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("Description:", description))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("MeasurementUnits:", res_unit))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("TimeUnits:", time_unit))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("Comments:", comment))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("Date:", date))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("Optimiser:", optimiser))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("[Data]")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in seq_along(ds)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste("NewDataSet:", names(ds)[i]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d <- mkin_long_to_wide(ds[[i]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(d) <- c("Time", map[names(d)[-1]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> write.table(d, csf,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sep = "\t", col.names = TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = FALSE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> quote = FALSE, eol = "\r\n", na = "")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(links)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("[Model]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste0("ParentCompartment: Parent\t", names(map)[1], "\t", names(map)[1]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (name in names(map)[-1]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste0("Compartment: ", map[name], "\t", name, "\t", name))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (li in names(links)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste0("Link: ", map[li], "\t", map[links[li]], "\t0.5\t0\t1\tFree\tExplicit"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add("[ComponentNames]")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (name in names(map)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> add(paste0(map[name], ":", name))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/summary_listing.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Display the output of a summary function according to the output format</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function is intended for use in a R markdown code chunk with the chunk</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' option `results = "asis"`.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The object for which the summary is to be listed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param caption An optional caption</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param label An optional label, ignored in html output</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param clearpage Should a new page be started after the listing? Ignored in html output</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">summary_listing <- function(object, caption = NULL, label = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> clearpage = TRUE) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">13</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (knitr::is_latex_output()) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">14</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> tex_listing(object = object, caption = caption, label = label,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">15</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> clearpage = clearpage)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">17</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (knitr::is_html_output()) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">18</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> html_listing(object = object, caption = caption)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary_listing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">tex_listing <- function(object, caption = NULL, label = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> clearpage = TRUE) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">26</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">27</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\begin{listing}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">28</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(caption)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">29</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\caption{", caption, "}", "\n", sep = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">31</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(label)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">32</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\caption{", label, "}", "\n", sep = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">34</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\begin{snugshade}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">35</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\scriptsize", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">36</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\begin{verbatim}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">37</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat(capture.output(suppressWarnings(summary(object))), sep = "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">38</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">39</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\end{verbatim}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">40</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\end{snugshade}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">41</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\end{listing}", "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">42</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (clearpage) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">43</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\\clearpage", "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary_listing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">html_listing <- function(object, caption = NULL) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">50</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">51</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(caption)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">52</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<caption>", caption, "</caption>", "\n", sep = "")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">54</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<pre><code>\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">55</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat(capture.output(suppressWarnings(summary(object))), sep = "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">56</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">57</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("</pre></code>\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/multistart.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Perform a hierarchical model fit with multiple starting values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The purpose of this method is to check if a certain algorithm for fitting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nonlinear hierarchical models (also known as nonlinear mixed-effects models)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' will reliably yield results that are sufficiently similar to each other, if</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' started with a certain range of reasonable starting parameters. It is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' inspired by the article on practical identifiabiliy in the frame of nonlinear</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mixed-effects models by Duchesne et al (2021).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The fit object to work with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param n How many different combinations of starting parameters should be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' used?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cores How many fits should be run in parallel (only on posix platforms)?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cluster A cluster as returned by [parallel::makeCluster] to be used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for parallel execution.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Passed to the update function.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x The multistart object to print</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list of [saem.mmkin] objects, with class attributes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 'multistart.saem.mmkin' and 'multistart'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [parplot], [llhist]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' identifiability in the frame of nonlinear mixed effects models: the example</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' doi: 10.1186/s12859-021-04373-4.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(mkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dmta_ds <- lapply(1:7, function(i) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_i <- dimethenamid_2018$ds[[i]]$data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_i[ds_i$name == "DMTAP", "name"] <- "DMTA"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_i</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_full <- saem(f_mmkin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parplot(f_saem_full_multi, lpos = "topleft")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_full)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_reduced)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # On Windows, we need to create a PSOCK cluster first and refer to it</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # in the call to multistart()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(parallel)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cl <- makePSOCKcluster(12)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' stopCluster(cl)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">multistart <- function(object, n = 50,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cluster = NULL, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("multistart", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">multistart.saem.mmkin <- function(object, n = 50, cores = 1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cluster = NULL, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- match.call()</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">68</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n <= 1) stop("Please specify an n of at least 2")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mmkin_object <- object$mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mmkin_parms <- parms(mmkin_object, errparms = FALSE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> transformed = object$transformations == "mkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> start_parms <- apply(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mmkin_parms, 1,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(x) stats::runif(n, min(x), max(x)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call <- object$call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call[[1]] <- saem</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call[[2]] <- mmkin_object</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> i_startparms <- which(names(saem_call) == "degparms_start")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fit_function <- function(x) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> new_startparms <- str2lang(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste0(capture.output(dput(start_parms[x, ])),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> collapse = ""))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(i_startparms) == 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call <- c(as.list(saem_call), degparms_start = new_startparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call <- as.call(saem_call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">93</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> saem_call[i_startparms] <- new_startparms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret <- eval(saem_call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ret)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(cluster)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- parallel::mclapply(1:n, fit_function,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">200<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mc.cores = cores, mc.preschedule = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">105</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> res <- parallel::parLapplyLB(cluster, 1:n, fit_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(res, "orig") <- object</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(res, "start_parms") <- start_parms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(res, "call") <- call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(res) <- c("multistart.saem.mmkin", "multistart")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">status.multistart <- function(object, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">116</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> all_summary_warnings <- character()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">118</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">119</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> function(fit) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">120</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit, "try-error")) return("E")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">122</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return("OK")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">125</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">127</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "status.multistart"</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">128</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">130</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">status.multistart.saem.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_summary_warnings <- character()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- lapply(object,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> function(fit) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">137</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(fit$so, "try-error")) return("E")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">704<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return("OK")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> })</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- unlist(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(result) <- "status.multistart"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.status.multistart <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(x) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(table(x, dnn = NULL))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "OK")) cat("OK: Fit terminated successfully\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">153</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x == "E")) cat("E: Error\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.multistart <- function(x, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<multistart> object with", length(x), "fits:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">88<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(status(x))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">best <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("best", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The object with the highest likelihood</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">best.default <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">184<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(object[[which.best(object)]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The index of the object with the highest likelihood</pre> + </td> + </tr> + <tr class="never"> + <td class="num">179</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">181</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">which.best <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">360<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("which.best", object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">which.best.default <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">360<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llfunc <- function(object) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">191</td> + <td class="coverage">2528<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ret <- try(logLik(object))</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">192</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(ret, "try-error")) return(NA)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">193</td> + <td class="coverage">2528<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(ret)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">360<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll <- sapply(object, llfunc)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">360<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(which.max(ll))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.multistart <- function(object, ..., evaluate = TRUE) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">201</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call <- attr(object, "call")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # For some reason we get multistart.saem.mmkin in call[[1]] when using multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # from the loaded package so we need to fix this so we do not have to export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">204</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # multistart.saem.mmkin</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">205</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call[[1]] <- multistart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">207</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments <- match.call(expand.dots = FALSE)$...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">209</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(update_arguments) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">210</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_in_call <- !is.na(match(names(update_arguments), names(call)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">213</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (a in names(update_arguments)[update_arguments_in_call]) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">214</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call[[a]] <- update_arguments[[a]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">217</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_not_in_call <- !update_arguments_in_call</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">218</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if(any(update_arguments_not_in_call)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">219</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call <- c(as.list(call), update_arguments[update_arguments_not_in_call])</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">220</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> call <- as.call(call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">222</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if(evaluate) eval(call, parent.frame())</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">223</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/lrtest.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom lmtest lrtest</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">lmtest::lrtest</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Likelihood ratio test for mkinfit models</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Compare two mkinfit models based on their likelihood. If two fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinfit objects are given as arguments, it is checked if they have been</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fitted to the same data. It is the responsibility of the user to make sure</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' that the models are nested, i.e. one of them has less degrees of freedom</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and can be expressed by fixing the parameters of the other.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Alternatively, an argument to mkinfit can be given which is then passed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to \code{\link{update.mkinfit}} to obtain the alternative model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The comparison is then made by the \code{\link[lmtest]{lrtest.default}}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method from the lmtest package. The model with the higher number of fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters (alternative hypothesis) is listed first, then the model with the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lower number of fitted parameters (null hypothesis).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats logLik update</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An \code{\link{mkinfit}} object, or an \code{\link{mmkin}} column</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' object containing two fits to the same data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object_2 Optionally, another mkinfit object fitted to the same data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Argument to \code{\link{mkinfit}}, passed to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{update.mkinfit}} for creating the alternative fitted object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(dfop_fit, sfo_fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(sfo_fit, dfop_fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The following two examples are commented out as they fail during</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # generation of the static help pages by pkgdown</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #lrtest(dfop_fit, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #lrtest(dfop_fit, fixed_parms = c(k2 = 0))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # However, this equivalent syntax also works for static help pages</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(dfop_fit, update(dfop_fit, error_model = "tc"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">lrtest.mkinfit <- function(object, object_2 = NULL, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">6<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name_function <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_name <- paste(x$mkinmod$name, "with error model", x$err_mod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(x$bparms.fixed) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">7<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_name <- paste(object_name,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">7<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "and fixed parameter(s)",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">7<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste(names(x$bparms.fixed), collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(object_name)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">6<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(object_2)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">58</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object_2 <- update(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">6<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_object <- object$data[c("time", "variable", "observed")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">6<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_object_2 <- object_2$data[c("time", "variable", "observed")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">6<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(data_object, data_object_2)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("It seems that the mkinfit objects have not been fitted to the same data")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (attr(logLik(object), "df") > attr(logLik(object_2), "df")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lmtest::lrtest.default(object, object_2, name = name_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lmtest::lrtest.default(object_2, object, name = name_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname lrtest.mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">lrtest.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">76</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) != 2 | ncol(object) > 1) stop("Only works for a column containing two mkinfit objects")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">77</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object[[1, 1]]$mkinmod$name <- rownames(object)[1]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">78</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object[[2, 1]]$mkinmod$name <- rownames(object)[2]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">79</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> lrtest(object[[1, 1]], object[[2, 1]])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/aw.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculate Akaike weights for model averaging</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Akaike weights are calculated based on the relative</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' expected Kullback-Leibler information as specified</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' by Burnham and Anderson (2004).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An [mmkin] column object, containing two or more</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' [mkinfit] models that have been fitted to the same data,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' or an mkinfit object. In the latter case, further mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' objects fitted to the same data should be specified</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as dots arguments.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used in the method for [mmkin] column objects,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' further [mkinfit] objects in the method for mkinfit objects.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Burnham KP and Anderson DR (2004) Multimodel</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Inference: Understanding AIC and BIC in Model Selection.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' *Sociological Methods & Research* **33**(2) 261-304</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @md</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_sfo <- mkinfit("SFO", FOCUS_2006_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_dfop <- mkinfit("DFOP", FOCUS_2006_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' aw_sfo_dfop <- aw(f_sfo, f_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sum(aw_sfo_dfop)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin(c("SFO", "FOMC", "DFOP"), list("FOCUS D" = FOCUS_2006_D), cores = 1, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' aw(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sum(aw(f))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' aw(f[c("SFO", "DFOP")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">1482<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r">aw <- function(object, ...) UseMethod("aw")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">.aw <- function(all_objects) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> AIC_all <- sapply(all_objects, AIC)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> delta_i <- AIC_all - min(AIC_all)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">36</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> denom <- sum(exp(-delta_i/2))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">37</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> w_i <- exp(-delta_i/2) / denom</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(w_i)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname aw</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">aw.mkinfit <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">988<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oo <- list(...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">988<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_object <- object$data[c("time", "variable", "observed")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">988<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in seq_along(oo)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(oo[[i]], "mkinfit")) stop("Please supply only mkinfit objects")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">988<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_other_object <- oo[[i]]$data[c("time", "variable", "observed")]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">988<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(data_object, data_other_object)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("It seems that the mkinfit objects have not all been fitted to the same data")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_objects <- list(object, ...)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> .aw(all_objects)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname aw</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">aw.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ncol(object) > 1) stop("Please supply an mmkin column object")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> do.call(aw, object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname aw</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">aw.mixed.mmkin <- function(object, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">67</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> oo <- list(...)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">68</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> data_object <- object$data[c("ds", "name", "time", "value")]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">69</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in seq_along(oo)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">70</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!inherits(oo[[i]], "mixed.mmkin")) stop("Please supply objects inheriting from mixed.mmkin")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">71</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> data_other_object <- oo[[i]]$data[c("ds", "name", "time", "value")]</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">72</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(data_object, data_other_object)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">73</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("It seems that the mixed.mmkin objects have not all been fitted to the same data")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">76</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> all_objects <- list(object, ...)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">77</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> .aw(all_objects)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname aw</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">aw.multistart <- function(object, ...) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">83</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> do.call(aw, object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mean_degparms.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculate mean degradation parameters for an mmkin row object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return If random is FALSE (default), a named vector containing mean values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the fitted degradation model parameters. If random is TRUE, a list with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fixed and random effects, in the format required by the start argument of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' nlme for the case of a single grouping variable ds.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An mmkin row object containing several fits of the same model to different datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param random Should a list with fixed and random effects be returned?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param test_log_parms If TRUE, log parameters are only considered in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the mean calculations if their untransformed counterparts (most likely</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rate constants) pass the t-test for significant difference from zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param conf.level Possibility to adjust the required confidence level</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for parameter that are tested if requested by 'test_log_parms'.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param default_log_parms If set to a numeric value, this is used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as a default value for the tested log parameters that failed the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' t-test.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mean_degparms <- function(object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> default_log_parms = NA)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">21</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(object) > 1) stop("Only row objects allowed")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">22</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_trans <- sapply(object, parms, transformed = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (test_log_parms) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_dim <- dim(parm_mat_trans)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">26</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_dimnames <- dimnames(parm_mat_trans)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> log_parm_trans_names <- grep("^log_", rownames(parm_mat_trans), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> log_parm_names <- gsub("^log_", "", log_parm_trans_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t_test_back_OK <- matrix(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sapply(object, function(o) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">49860<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> suppressWarnings(summary(o)$bpar[log_parm_names, "Pr(>t)"] < (1 - conf.level))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> }), nrow = length(log_parm_names))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(t_test_back_OK) <- log_parm_trans_names</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">37</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_trans_OK <- parm_mat_trans</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">4668<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (trans_parm in log_parm_trans_names) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">9398<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_trans_OK[trans_parm, ] <- ifelse(t_test_back_OK[trans_parm, ],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">9398<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_trans[trans_parm, ], log(default_log_parms))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">2603<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm_mat_trans_OK <- parm_mat_trans</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mean_degparm_names <- setdiff(rownames(parm_mat_trans), names(object[[1]]$errparms))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_mat_trans <- parm_mat_trans[mean_degparm_names, , drop = FALSE]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> degparm_mat_trans_OK <- parm_mat_trans_OK[mean_degparm_names, , drop = FALSE]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # fixed in the sense of fixed effects, as this function was</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # written to supply starting parameters for nlme</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed <- apply(degparm_mat_trans_OK, 1, mean, na.rm = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">7271<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (random) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">2322<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> random <- t(apply(degparm_mat_trans[mean_degparm_names, , drop = FALSE], 2, function(column) column - fixed))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # If we only have one parameter, apply returns a vector so we get a single row</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">56</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (nrow(degparm_mat_trans) == 1) random <- t(random)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">2322<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(random) <- levels(nlme_data(object)$ds)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # For nlmixr we can specify starting values for standard deviations eta, and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # we ignore uncertain parameters if test_log_parms is FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">2322<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> eta <- apply(degparm_mat_trans_OK, 1, stats::sd, na.rm = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">2322<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(list(fixed = fixed, random = list(ds = random), eta = eta))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">4949<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(fixed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/ilr.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># This file is part of the R package mkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># mkin is free software: you can redistribute it and/or modify it under the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># terms of the GNU General Public License as published by the Free Software</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># Foundation, either version 3 of the License, or (at your option) any later</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># version.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># This program is distributed in the hope that it will be useful, but WITHOUT</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># FOR A PARTICULAR PURPOSE. See the GNU General Public License for more</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># details.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># You should have received a copy of the GNU General Public License along with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"># this program. If not, see <http://www.gnu.org/licenses/></pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to perform isometric log-ratio transformation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This implementation is a special case of the class of isometric log-ratio</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformations.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @aliases ilr invilr</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x A numeric vector. Naturally, the forward transformation is only</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sensible for vectors with all elements being greater than zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The result of the forward or backward transformation. The returned</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' components always sum to 1 for the case of the inverse log-ratio</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author René Lehmann and Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso Another implementation can be found in R package</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{robCompositions}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Peter Filzmoser, Karel Hron (2008) Outlier Detection for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Compositional Data Using Robust Methods. Math Geosci 40 233-248</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @keywords manip</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Order matters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ilr(c(0.1, 1, 10))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ilr(c(10, 1, 0.1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Equal entries give ilr transformations with zeros as elements</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ilr(c(3, 3, 3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Almost equal entries give small numbers</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ilr(c(0.3, 0.4, 0.3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Only the ratio between the numbers counts, not their sum</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' invilr(ilr(c(0.7, 0.29, 0.01)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' invilr(ilr(2.1 * c(0.7, 0.29, 0.01)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Inverse transformation of larger numbers gives unequal elements</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' invilr(-10)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' invilr(c(-10, 0))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The sum of the elements of the inverse ilr is 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sum(invilr(c(-10, 0)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This is why we do not need all elements of the inverse transformation to go back:</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a <- c(0.1, 0.3, 0.5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' b <- invilr(a)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' length(b) # Four elements</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">ilr <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> z <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:(length(x) - 1)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">44<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> z[i] <- sqrt(i/(i+1)) * log((prod(x[1:i]))^(1/i) / x[i+1])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">16<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(z)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname ilr</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">invilr<-function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> D <- length(x) + 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> z <- c(x, 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> y <- rep(0, D)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> s <- sqrt(1:D*2:(D+1))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> q <- z/s</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> y[1] <- sum(q[1:D])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 2:D) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">1585969<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> y[i] <- sum(q[i:D]) - sqrt((i-1)/i) * z[i-1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> z <- vector()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:D) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">2115270<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> z[i] <- exp(y[i])/sum(exp(y))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Work around a numerical problem with NaN values returned by the above</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Only works if there is only one NaN value: replace it with 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # if the sum of the other components is < 1e-10</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (sum(is.na(z)) == 1 && sum(z[!is.na(z)]) < 1e-10)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">86</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> z = ifelse(is.na(z), 1, z)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">529301<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(z)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/max_twa_parent.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to calculate maximum time weighted average concentrations from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic models fitted with mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function calculates maximum moving window time weighted average</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' concentrations (TWAs) for kinetic models fitted with \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Currently, only calculations for the parent are implemented for the SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOMC, DFOP and HS models, using the analytical formulas given in the PEC</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' soil section of the FOCUS guidance.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @aliases max_twa_parent max_twa_sfo max_twa_fomc max_twa_dfop max_twa_hs</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fit An object of class \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param windows The width of the time windows for which the TWAs should be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' calculated.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param M0 The initial concentration for which the maximum time weighted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' average over the decline curve should be calculated. The default is to use</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a value of 1, which means that a relative maximum time weighted average</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' factor (f_twa) is calculated.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k The rate constant in the case of SFO kinetics.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param t The width of the time window.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha Parameter of the FOMC model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param beta Parameter of the FOMC model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k1 The first rate constant of the DFOP or the HS kinetics.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k2 The second rate constant of the DFOP or the HS kinetics.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param g Parameter of the DFOP model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param tb Parameter of the HS model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return For \code{max_twa_parent}, a numeric vector, named using the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{windows} argument. For the other functions, a numeric vector of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' length one (also known as 'a number').</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' max_twa_parent(fit, c(7, 21))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">max_twa_parent <- function(fit, windows) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.all <- c(fit$bparms.optim, fit$bparms.fixed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_vars <- fit$obs_vars</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(obs_vars) > 1) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">45</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> warning("Calculation of maximum time weighted average concentrations is",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">46</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "currently only implemented for the parent compound using",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">47</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "analytical solutions")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_var <- obs_vars[1]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> spec = fit$mkinmod$spec</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> type = spec[[1]]$type</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> M0 <- parms.all[paste0(obs_var, "_0")]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "SFO") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k_name <- paste0("k_", obs_var)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (fit$mkinmod$use_of_ff == "min") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">58</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> k_name <- paste0(k_name, "_sink")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k <- parms.all[k_name]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> twafunc <- function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max_twa_sfo(M0, k, t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "FOMC") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> alpha <- parms.all["alpha"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> beta <- parms.all["beta"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> twafunc <- function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max_twa_fomc(M0, alpha, beta, t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "DFOP") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- parms.all["k1"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- parms.all["k2"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> g <- parms.all["g"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> twafunc <- function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max_twa_dfop(M0, k1, k2, g, t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type == "HS") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k1 <- parms.all["k1"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> k2 <- parms.all["k2"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tb <- parms.all["tb"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> twafunc <- function(t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(t <= tb,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max_twa_sfo(M0, k1, t),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> max_twa_hs(M0, k1, k2, tb, t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type %in% c("IORE", "SFORB")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">92</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Calculation of maximum time weighted average concentrations is currently ",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">93</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "not implemented for the ", type, " model.")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- twafunc(windows)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(res) <- windows</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname max_twa_parent</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">max_twa_sfo <- function(M0 = 1, k, t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> M0 * (1 - exp(- k * t)) / (k * t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname max_twa_parent</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">max_twa_fomc <- function(M0 = 1, alpha, beta, t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> M0 * (beta)/(t * (1 - alpha)) * ((t/beta + 1)^(1 - alpha) - 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname max_twa_parent</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">max_twa_dfop <- function(M0 = 1, k1, k2, g, t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname max_twa_parent</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">max_twa_hs <- function(M0 = 1, k1, k2, tb, t) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">121</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (M0 / t) * (</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (1/k1) * (1 - exp(- k1 * tb)) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (exp(- k1 * tb) / k2) * (1 - exp(- k2 * (t - tb)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/f_time_norm_focus.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables("D24_2014")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Normalisation factors for aerobic soil degradation according to FOCUS guidance</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Time step normalisation factors for aerobic soil degradation as described</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An object containing information used for the calculations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param temperature Numeric vector of temperatures in °C</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param moisture Numeric vector of moisture contents in \\% w/w</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param field_moisture Numeric vector of moisture contents at field capacity</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (pF2) in \\% w/w</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param study_moisture_ref_source Source for the reference value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' used to calculate the study moisture. If 'auto', preference is given</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to a reference moisture given in the meta information, otherwise</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the focus soil moisture for the soil class is used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param Q10 The Q10 value used for temperature normalisation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param walker The Walker exponent used for moisture normalisation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param f_na The factor to use for NA values. If set to NA, only factors</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for complete cases will be returned.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Currently not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Version 1.1, 18 December 2014</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [focus_soil_moisture]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_time_norm_focus(25, 20, 25) # 1.37, compare FOCUS 2014 p. 184</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' D24_2014$meta</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # No moisture normalisation in the first dataset, so we use f_na = 1 to get</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # temperature only normalisation as in the EU evaluation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_time_norm_focus(D24_2014, study_moisture_ref_source = "focus", f_na = 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">f_time_norm_focus <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">765<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("f_time_norm_focus")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname f_time_norm_focus</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">f_time_norm_focus.numeric <- function(object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> moisture = NA, field_moisture = NA,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> temperature = object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> Q10 = 2.58, walker = 0.7, f_na = NA, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_temp <- ifelse(is.na(temperature),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_na,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(temperature <= 0,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> 0,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Q10^((temperature - 20)/10)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_moist <- ifelse(is.na(moisture),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_na,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(moisture >= field_moisture,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> 1,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (moisture / field_moisture)^walker))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_time_norm <- f_temp * f_moist</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">459<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_time_norm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname f_time_norm_focus</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">f_time_norm_focus.mkindsg <- function(object,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref_source = c("auto", "meta", "focus"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> Q10 = 2.58, walker = 0.7, f_na = NA, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref_source <- match.arg(study_moisture_ref_source)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> meta <- object$meta</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(meta$field_moisture)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> field_moisture <- focus_soil_moisture[meta$usda_soil_type, "pF2"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">79</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> field_moisture <- ifelse(is.na(meta$field_moisture),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">80</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> focus_soil_moisture[meta$usda_soil_type, "pF2"],</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">81</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> meta$field_moisture)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref_focus <-</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> focus_soil_moisture[as.matrix(meta[c("usda_soil_type", "study_moisture_ref_type")])]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (study_moisture_ref_source == "auto") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref <- ifelse (is.na(meta$study_ref_moisture),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref_focus,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> meta$study_ref_moisture)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (study_moisture_ref_source == "meta") {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">93</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref <- meta$study_moisture_ref</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">153<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture_ref <- study_moisture_ref_focus</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if ("study_moisture" %in% names(meta)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">100</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture <- ifelse(is.na(meta$study_moisture),</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">101</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> meta$rel_moisture * study_moisture_ref,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">102</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> meta$study_moisture)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> study_moisture <- meta$rel_moisture * study_moisture_ref</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$f_time_norm <- f_time_norm_focus(meta$temperature,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> moisture = study_moisture, field_moisture = field_moisture,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> Q10 = Q10, walker = walker, f_na = f_na)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> message("$f_time_norm was (re)set to normalised values")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">306<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(object$f_time_norm)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinds.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A dataset class for mkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @description</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' At the moment this dataset class is hardly used in mkin. For example,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinfit does not take mkinds datasets as argument, but works with dataframes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' such as the on contained in the data field of mkinds objects. Some datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' provided by this package come as mkinds objects nevertheless.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom R6 R6Class</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mds <- mkinds$new("FOCUS A", FOCUS_2006_A)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(mds)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinds <- R6Class("mkinds",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> public = list(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field title A full title for the dataset</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> title = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field sampling_times The sampling times</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> sampling_times = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field time_unit The time unit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> time_unit = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field observed Names of the observed variables</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> observed = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field unit The unit of the observations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> unit = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field replicates The maximum number of replicates per sampling time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> replicates = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field data A data frame with at least the columns name, time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' and value in order to be compatible with mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> data = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @description</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' Create a new mkinds object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param title The dataset title</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param data The data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param time_unit The time unit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param unit The unit of the observations</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> initialize = function(title = "", data, time_unit = NA, unit = NA) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$title <- title</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$sampling_times <- sort(unique(data$time))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$time_unit <- time_unit</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$observed <- unique(data$name)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$unit <- unit</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$replicates <- max(by(data, list(data$name, data$time), nrow))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(data$override)) data$override <- NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(data$err)) data$err <- 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">57</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$data <- data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print mkinds objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkinds</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An [mkinds] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data Should the data be printed?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mkinds <- function(x, data = FALSE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<mkinds> with $title: ", x$title, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Observed compounds $observed: ", paste(x$observed, collapse = ", "), "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Sampling times $sampling_times:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(paste(x$sampling_times, collapse = ", "), "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("With a maximum of ", x$replicates, " replicates\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(x$time_unit)) cat("Time unit: ", x$time_unit, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(x$unit)) cat("Observation unit: ", x$unit, "\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">78</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (data) print(mkin_long_to_wide(x$data))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A class for dataset groups for mkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @description</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A container for working with datasets that share at least one compound,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' so that combined evaluations are desirable.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Time normalisation factors are initialised with a value of 1 for each</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dataset if no data are supplied.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mdsg <- mkindsg$new("Experimental X", experimental_data_for_UBA_2019[6:10])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(mdsg)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(mdsg, verbose = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(mdsg, verbose = TRUE, data = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkindsg <- R6Class("mkindsg",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> public = list(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field title A title for the dataset group</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> title = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field ds A list of mkinds objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ds = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field observed_n Occurrence counts of compounds in datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> observed_n = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field f_time_norm Time normalisation factors</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> f_time_norm = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @field meta A data frame with a row for each dataset,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' containing additional information in the form</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' of categorical data (factors) or numerical data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' (e.g. temperature, moisture,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' or covariates like soil pH).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> meta = NULL,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @description</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' Create a new mkindsg object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param title The title</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param ds A list of mkinds objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param f_time_norm Time normalisation factors</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> #' @param meta The meta data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> initialize = function(title = "", ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> f_time_norm = rep(1, length(ds)), meta)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$title <- title</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(sapply(ds, inherits, "mkinds"))) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$ds <- ds</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">133</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please supply a list of mkinds objects")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_observed <- unlist(lapply(ds, function(x) x$observed))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> observed <- factor(all_observed, levels = unique(all_observed))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$observed_n <- table(observed)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(dimnames(self$observed_n)) <- NULL</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> self$f_time_norm <- f_time_norm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!missing(meta)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">143</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(meta) <- lapply(ds, function(x) x$title)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">144</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> self$meta <- meta</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Print mkindsg objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkindsg</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x An [mkindsg] object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose Should the mkinds objects be printed?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data Should the mkinds objects be printed with their data?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.mkindsg <- function(x, data = FALSE, verbose = data, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("<mkindsg> holding", length(x$ds), "mkinds objects\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Title $title: ", x$title, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Occurrence of observed compounds $observed_n:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$observed_n)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (any(x$f_time_norm != 1)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">164</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Time normalisation factors $f_time_norm:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">165</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$f_time_norm)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$meta)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Meta information $meta:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">104<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$meta)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">208<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (verbose) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">172</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nDatasets $ds:")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">173</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> for (ds in x$ds) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">174</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">175</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(ds, data = data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">177</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinerrmin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("name", "value_mean"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculate the minimum error to assume in order to pass the variance test</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function finds the smallest relative error still resulting in passing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the chi-squared test as defined in the FOCUS kinetics report from 2006.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function is used internally by \code{\link{summary.mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param fit an object of class \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha The confidence level chosen for the chi-squared test.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats qchisq aggregate</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A dataframe with the following components: \item{err.min}{The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' relative error, expressed as a fraction.} \item{n.optim}{The number of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' optimised parameters attributed to the data series.} \item{df}{The number of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' remaining degrees of freedom for the chi2 error level calculations. Note</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' that mean values are used for the chi2 statistic and therefore every time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' point with observed values in the series only counts one time.} The</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dataframe has one row for the total dataset and one further row for each</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed state variable in the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Registration} Report of the FOCUS Work Group on Degradation Kinetics, EC</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @keywords manip</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' round(mkinerrmin(fit_FOCUS_D), 4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' round(mkinerrmin(fit_FOCUS_E), 4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinerrmin <- function(fit, alpha = 0.05)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms.optim <- fit$par</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> kinerrmin <- function(errdata, n.parms) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">124726<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> means.mean <- mean(errdata$observed, na.rm = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">124726<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> df = nrow(errdata) - n.parms</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">124726<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err.min <- sqrt((1 / qchisq(1 - alpha, df)) *</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">124726<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sum((errdata$observed - errdata$predicted)^2)/(means.mean^2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">124726<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(list(err.min = err.min, n.optim = n.parms, df = df))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errdata <- aggregate(cbind(observed, predicted) ~ time + variable, data = fit$data, mean, na.rm=TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errdata <- errdata[order(errdata$time, errdata$variable), ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Remove values at time zero for variables whose value for state.ini is fixed,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # as these will not have any effect in the optimization and should therefore not</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # be counted as degrees of freedom.</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed_initials = gsub("_0$", "", rownames(subset(fit$fixed, type == "state")))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errdata <- subset(errdata, !(time == 0 & variable %in% fixed_initials))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.optim.overall <- length(parms.optim) - length(fit$errparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin.overall <- kinerrmin(errdata, n.optim.overall)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin <- data.frame(err.min = errmin.overall$err.min,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.optim = errmin.overall$n.optim, df = errmin.overall$df)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(errmin) <- "All data"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # The degrees of freedom are counted according to FOCUS kinetics (2011, p. 164)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (obs_var in fit$obs_vars)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">74</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errdata.var <- subset(errdata, variable == obs_var)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check if initial value is optimised</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.initials.optim <- length(grep(paste(obs_var, ".*", "_0", sep=""), names(parms.optim)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Rate constants and IORE exponents are attributed to the source variable</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.k.optim <- length(grep(paste("^k", obs_var, sep="_"), names(parms.optim)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.k.optim <- n.k.optim + length(grep(paste("^log_k", obs_var, sep="_"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(parms.optim)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.k__iore.optim <- length(grep(paste("^k__iore", obs_var, sep="_"), names(parms.optim)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.k__iore.optim <- n.k__iore.optim + length(grep(paste("^log_k__iore",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs_var, sep = "_"), names(parms.optim)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.N.optim <- length(grep(paste("^N", obs_var, sep="_"), names(parms.optim)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.ff.optim <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Formation fractions are attributed to the target variable, so look</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # for source compartments with formation fractions</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (source_var in fit$obs_vars) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">112543<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.ff.source = length(grep(paste("^f", source_var, sep = "_"),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">112543<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(parms.optim)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">112543<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.paths.source = length(fit$mkinmod$spec[[source_var]]$to)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">112543<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (target_var in fit$mkinmod$spec[[source_var]]$to) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">46296<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (obs_var == target_var) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">17974<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.ff.optim <- n.ff.optim + n.ff.source/n.paths.source</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.optim <- sum(n.initials.optim, n.k.optim, n.k__iore.optim, n.N.optim, n.ff.optim)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # FOMC, DFOP and HS parameters are only counted if we are looking at the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # first variable in the model which is always the source variable</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (obs_var == fit$obs_vars[[1]]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> special_parms = c("alpha", "log_alpha", "beta", "log_beta",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "k1", "log_k1", "k2", "log_k2",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "g", "g_ilr", "g_qlogis", "tb", "log_tb")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.optim <- n.optim + length(intersect(special_parms, names(parms.optim)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Calculate and add a line to the dataframe holding the results</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin.tmp <- kinerrmin(errdata.var, n.optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">70783<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmin[obs_var, c("err.min", "n.optim", "df")] <- errmin.tmp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">119</td> + <td class="coverage">53943<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(errmin)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/residuals.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Extract residuals from an mkinfit model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A \code{\link{mkinfit}} object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param standardized Should the residuals be standardized by dividing by the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' standard deviation obtained from the fitted error model?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mkinfit("DFOP", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' residuals(f)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' residuals(f, standardized = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">residuals.mkinfit <- function(object, standardized = FALSE, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">13</td> + <td class="coverage">2493<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- object$data[["residual"]]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">14</td> + <td class="coverage">2493<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (standardized) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">15</td> + <td class="coverage">2428<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "const") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">16</td> + <td class="coverage">543<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_fitted <- object$errparms["sigma"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">18</td> + <td class="coverage">2428<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "obs") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">19</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_names = paste0("sigma_", object$data[["variable"]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">20</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_fitted <- object$errparms[sigma_names]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">22</td> + <td class="coverage">2428<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$err_mod == "tc") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">23</td> + <td class="coverage">1820<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_fitted <- sigma_twocomp(object$data[["predicted"]],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">1820<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_low = object$errparms[1],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">1820<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rsd_high = object$errparms[2])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">2428<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res / sigma_fitted)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">65<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/AIC.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculate the AIC for a column of an mmkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Provides a convenient way to compare different kinetic models fitted to the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' same dataset.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats AIC BIC</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An object of class \code{\link{mmkin}}, containing only one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' column.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For compatibility with the generic method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k As in the generic method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return As in the generic method (a numeric value for single fits, or a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dataframe if there are several fits in the column).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{ # skip, as it takes > 10 s on winbuilder</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mmkin(c("SFO", "FOMC", "DFOP"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' list("FOCUS A" = FOCUS_2006_A,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We get a warning because the FOMC model does not converge for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # FOCUS A dataset, as it is well described by SFO</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f["SFO", "FOCUS A"]) # We get a single number for a single fit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f[["SFO", "FOCUS A"]]) # or when extracting an mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # For FOCUS A, the models fit almost equally well, so the higher the number</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # of parameters, the higher (worse) the AIC</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f[, "FOCUS A"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' BIC(f[, "FOCUS A"]) # Comparing the BIC gives a very similar picture</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # For FOCUS C, the more complex models fit better</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f[, "FOCUS C"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' BIC(f[, "FOCUS C"])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">AIC.mmkin <- function(object, ..., k = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We can only handle a single column</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ncol(object) != 1) stop("Please provide a single column object")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.fits <- length(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_names <- rownames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> code <- paste0("AIC(",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste0("object[[", 1:n.fits, "]]", collapse = ", "),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ", k = k)")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- eval(parse(text = code))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.fits > 1) rownames(res) <- model_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname AIC.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">BIC.mmkin <- function(object, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # We can only handle a single column</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ncol(object) != 1) stop("Please provide a single column object")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.fits <- length(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> model_names <- rownames(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> code <- paste0("BIC(",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> paste0("object[[", 1:n.fits, "]]", collapse = ", "),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ")")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- eval(parse(text = code))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (n.fits > 1) rownames(res) <- model_names</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">247<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/intervals.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom nlme intervals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">nlme::intervals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Confidence intervals for parameters in saem.mmkin objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The fitted saem.mmkin object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param level The confidence level. Must be the default of 0.95 as this is what</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' is available in the saemix object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param backtransform In case the model was fitted with mkin transformations,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' should we backtransform the parameters where a one to one correlation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' between transformed and backtransformed parameters exists?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For compatibility with the generic method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object with 'intervals.saem.mmkin' and 'intervals.lme' in the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' class attribute</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">intervals.saem.mmkin <- function(object, level = 0.95, backtransform = TRUE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">19</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!identical(level, 0.95)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">20</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Confidence intervals are only available for a level of 95%")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">23</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(object$mkinmod$diffs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pnames <- names(object$mean_dp_start)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Confidence intervals are available in the SaemixObject, so</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # we just need to extract them and put them into a list modelled</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # after the result of nlme::intervals.lme</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- object$so@results@conf.int</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(conf.int) <- conf.int$name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(conf.int)[2] <- "est."</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_trans <- as.matrix(conf.int[pnames, c("lower", "est.", "upper")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Fixed effects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # In case objects were produced by earlier versions of saem</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">38</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(object$transformations)) object$transformations <- "mkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$transformations == "mkin" & backtransform) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates, object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpnames <- names(bp)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform boundaries of CI for one parameter at a time,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # with the exception of sets of formation fractions (single fractions are OK).</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names_skip <- character(0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) { # Figure out sets of fractions to skip</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">2396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">2396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_paths <- length(f_names)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">51</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back <- matrix(NA, nrow = length(bp), ncol = 3,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(bpnames, colnames(confint_trans)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[, "est."] <- bp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in pnames) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!pname %in% f_names_skip) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.lower <- confint_trans[pname, "lower"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.upper <- confint_trans[pname, "upper"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(par.lower) <- names(par.upper) <- pname</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">63</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpl <- backtransform_odeparms(par.lower, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpu <- backtransform_odeparms(par.upper, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpl), "lower"] <- bpl</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">6314<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpu), "upper"] <- bpu</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">2286<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_ret <- confint_back</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">195<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_ret <- confint_trans</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(confint_ret, "label") <- "Fixed effects:"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Random effects</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">80</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sdnames <- intersect(rownames(conf.int), paste("SD", pnames, sep = "."))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> corrnames <- grep("^Corr.", rownames(conf.int), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ranef_ret <- as.matrix(conf.int[c(sdnames, corrnames), c("lower", "est.", "upper")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sdnames_ret <- paste0(gsub("SD\\.", "sd(", sdnames), ")")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">84</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> corrnames_ret <- gsub("Corr\\.(.*)\\.(.*)", "corr(\\1,\\2)", corrnames)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(ranef_ret) <- c(sdnames_ret, corrnames_ret)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(ranef_ret, "label") <- "Random effects:"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Error model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> enames <- if (object$err_mod == "const") "a.1" else c("a.1", "b.1")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_ret <- as.matrix(conf.int[enames, c("lower", "est.", "upper")])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res <- list(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fixed = confint_ret,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> random = ranef_ret,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errmod = err_ret</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> )</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(res) <- c("intervals.saemix.mmkin", "intervals.lme")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(res, "level") <- level</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">2481<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(res)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/update.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Update an mkinfit model with different arguments</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function will return an updated mkinfit object. The fitted degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model parameters from the old fit are used as starting values for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' updated fit. Values specified as 'parms.ini' and/or 'state.ini' will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' override these starting values.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An mkinfit object to be updated</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Arguments to \code{\link{mkinfit}} that should replace</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the arguments from the original call. Arguments set to NULL will</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' remove arguments given in the original call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param evaluate Should the call be evaluated or returned as a call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_err(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit_2 <- update(fit, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms(fit_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_err(fit_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">update.mkinfit <- function(object, ..., evaluate = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- object$call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments <- match.call(expand.dots = FALSE)$...</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get optimised ODE parameters and let parms.ini override them</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ode_optim_names <- intersect(names(object$bparms.optim), names(object$bparms.ode))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ode_start <- object$bparms.optim[ode_optim_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if ("parms.ini" %in% names(update_arguments)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">33</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ode_start[names(update_arguments["parms.ini"])] <- update_arguments["parms.ini"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ode_start)) update_arguments[["parms.ini"]] <- ode_start</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Get optimised values for initial states and let state.ini override them</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state_optim_names <- intersect(names(object$bparms.optim), paste0(names(object$bparms.state), "_0"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state_start <- object$bparms.optim[state_optim_names]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(state_start) <- gsub("_0$", "", names(state_start))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if ("state.ini" %in% names(update_arguments)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">42</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> state_start[names(update_arguments["state.ini"])] <- update_arguments["state.ini"]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(state_start)) update_arguments[["state.ini"]] <- state_start</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(update_arguments) > 0) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_in_call <- !is.na(match(names(update_arguments), names(call)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (a in names(update_arguments)[update_arguments_in_call]) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call[[a]] <- update_arguments[[a]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> update_arguments_not_in_call <- !update_arguments_in_call</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(any(update_arguments_not_in_call)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- c(as.list(call), update_arguments[update_arguments_not_in_call])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> call <- as.call(call)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(evaluate) eval(call, parent.frame())</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">60</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else call</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/confint.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Confidence intervals for parameters of mkinfit objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The default method 'quadratic' is based on the quadratic approximation of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the curvature of the likelihood function at the maximum likelihood parameter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' estimates.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The alternative method 'profile' is based on the profile likelihood for each</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameter. The 'profile' method uses two nested optimisations and can take a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' very long time, even if parallelized by specifying 'cores' on unixoid</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' platforms. The speed of the method could likely be improved by using the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' method of Venzon and Moolgavkar (1988).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An \code{\link{mkinfit}} object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param parm A vector of names of the parameters which are to be given</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' confidence intervals. If missing, all parameters are considered.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param level The confidence level required</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha The allowed error probability, overrides 'level' if specified.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cutoff Possibility to specify an alternative cutoff for the difference</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in the log-likelihoods at the confidence boundary. Specifying an explicit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cutoff value overrides arguments 'level' and 'alpha'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param method The 'quadratic' method approximates the likelihood function at</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the optimised parameters using the second term of the Taylor expansion,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' using a second derivative (hessian) contained in the object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The 'profile' method searches the parameter space for the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cutoff of the confidence intervals by means of a likelihood ratio test.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param transformed If the quadratic approximation is used, should it be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' applied to the likelihood based on the transformed parameters?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param backtransform If we approximate the likelihood in terms of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformed parameters, should we backtransform the parameters with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' their confidence intervals?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rel_tol If the method is 'profile', what should be the accuracy</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of the lower and upper bounds, relative to the estimate obtained from</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the quadratic method?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param cores The number of cores to be used for multicore processing.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' On Windows machines, cores > 1 is currently not supported.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param quiet Should we suppress the message "Profiling the likelihood"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A matrix with columns giving lower and upper confidence limits for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' each parameter.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats qnorm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Pawitan Y (2013) In all likelihood - Statistical modelling and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' inference using likelihood. Clarendon Press, Oxford.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Venzon DJ and Moolgavkar SH (1988) A Method for Computing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 87–94.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' confint(f, method = "quadratic")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' confint(f, method = "profile")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Set the number of cores for the profiling method for further examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (identical(Sys.getenv("NOT_CRAN"), "true")) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n_cores <- parallel::detectCores() - 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' } else {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n_cores <- 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (Sys.getenv("TRAVIS") != "") n_cores = 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (Sys.info()["sysname"] == "Windows") n_cores = 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "min", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "max", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' system.time(ci_profile <- confint(f_d_1, method = "profile", cores = 1, quiet = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Using more cores does not save much time here, as parent_0 takes up most of the time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # If we additionally exclude parent_0 (the confidence of which is often of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # minor interest), we get a nice performance improvement if we use at least 4 cores</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = "profile",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = n_cores))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_profile</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_transformed <- confint(f_d_1, method = "quadratic")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_transformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_untransformed <- confint(f_d_1, method = "quadratic", transformed = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_untransformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Against the expectation based on Bates and Watts (1988), the confidence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # intervals based on the internal parameter transformation are less</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # congruent with the likelihood based intervals. Note the superiority of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # interval based on the untransformed fit for k_m1_sink</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_transformed < rel_diffs_untransformed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' signif(rel_diffs_transformed, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' signif(rel_diffs_untransformed, 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Investigate a case with formation fractions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_d_2 <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_profile_ff <- confint(f_d_2, method = "profile", cores = n_cores)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_profile_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_transformed_ff <- confint(f_d_2, method = "quadratic")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_transformed_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_untransformed_ff <- confint(f_d_2, method = "quadratic", transformed = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ci_quadratic_untransformed_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_transformed_ff <- abs((ci_quadratic_transformed_ff - ci_profile_ff)/ci_profile_ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff)/ci_profile_ff)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # While the confidence interval for the parent rate constant is closer to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # the profile based interval when using the internal parameter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # transformation, the interval for the metabolite rate constant is 'better</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # without internal parameter transformation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_transformed_ff < rel_diffs_untransformed_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_transformed_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rel_diffs_untransformed_ff</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The profiling for the following fit does not finish in a reasonable time,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # therefore we use the quadratic approximation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = mkinsub("SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' use_of_ff = "max", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = "tc",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' error_model_algorithm = "direct", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' confint(f_tc_2, method = "quadratic")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' confint(f_tc_2, "parent_0", method = "quadratic")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">confint.mkinfit <- function(object, parm,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> level = 0.95, alpha = 1 - level, cutoff,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> method = c("quadratic", "profile"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> transformed = TRUE, backtransform = TRUE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> cores = parallel::detectCores(), rel_tol = 0.01, quiet = FALSE, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tparms <- parms(object, transformed = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bparms <- parms(object, transformed = FALSE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tpnames <- names(tparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpnames <- names(bparms)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_pnames <- if (missing(parm)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (backtransform) bpnames else tpnames</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> p <- length(return_pnames)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> method <- match.arg(method)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> a <- c(alpha / 2, 1 - (alpha / 2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> quantiles <- qt(a, object$df.residual)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar_pnames <- if (missing(parm)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">420<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformed) tpnames else bpnames</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_parms <- if (backtransform) bparms[return_pnames]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">155</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else tparms[return_pnames]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar_parms <- if (transformed) tparms[covar_pnames]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else bparms[covar_pnames]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformed) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">840<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar <- try(solve(object$hessian), silent = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">420<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> covar <- try(solve(object$hessian_notrans), silent = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # If inverting the covariance matrix failed or produced NA values</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.numeric(covar) | is.na(covar[1])) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">168</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> ses <- lci <- uci <- rep(NA, p)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">170</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ses <- sqrt(diag(covar))[covar_pnames]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">171</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci <- covar_parms + quantiles[1] * ses</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uci <- covar_parms + quantiles[2] * ses</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (transformed & backtransform) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci_back <- backtransform_odeparms(lci,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">175</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$mkinmod, object$transform_rates, object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uci_back <- backtransform_odeparms(uci,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$mkinmod, object$transform_rates, object$transform_fractions)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">178</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return_errparm_names <- intersect(names(object$errparms), return_pnames)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">180</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci <- c(lci_back, lci[return_errparm_names])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">630<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uci <- c(uci_back, uci[return_errparm_names])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">182</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">183</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ci <- cbind(lower = lci, upper = uci)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">1260<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (method == "profile") {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ci_quadratic <- ci</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!quiet) message("Profiling the likelihood")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci <- uci <- rep(NA, p)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">193</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(lci) <- names(uci) <- return_pnames</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> profile_pnames <- if(missing(parm)) names(parms(object))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else parm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">198</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (missing(cutoff)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cutoff <- 0.5 * qchisq(1 - alpha, 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">202</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> all_parms <- parms(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> get_ci <- function(pname) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pnames_free <- setdiff(names(all_parms), pname)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> profile_ll <- function(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">80<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pll_cost <- function(P) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">209</td> + <td class="coverage">3132<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_cost <- all_parms</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">3132<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_cost[pnames_free] <- P[pnames_free]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">3132<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parms_cost[pname] <- x</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">212</td> + <td class="coverage">3132<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> - object$ll(parms_cost)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">214</td> + <td class="coverage">80<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> - nlminb(all_parms[pnames_free], pll_cost)$objective</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cost <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">80<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (cutoff - (object$logLik - profile_ll(x)))^2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lower_quadratic <- ci_quadratic["lower"][pname]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper_quadratic <- ci_quadratic["upper"][pname]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">223</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ltol <- if (!is.na(lower_quadratic)) rel_tol * lower_quadratic else .Machine$double.eps^0.25</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> utol <- if (!is.na(upper_quadratic)) rel_tol * upper_quadratic else .Machine$double.eps^0.25</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lci_pname <- optimize(cost, lower = 0, upper = all_parms[pname], tol = ltol)$minimum</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">226</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> uci_pname <- optimize(cost, lower = all_parms[pname],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">227</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> upper = ifelse(grepl("^f_|^g$", pname), 1, 15 * all_parms[pname]),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tol = utol)$minimum</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(c(lci_pname, uci_pname))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">210<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ci <- t(parallel::mcmapply(get_ci, profile_pnames, mc.cores = cores))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">234</td> + <td class="coverage">1257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(ci) <- paste0(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">1257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> format(100 * a, trim = TRUE, scientific = FALSE, digits = 3), "%")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">1257<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(ci)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/set_nd_nq.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Set non-detects and unquantified values in residue series without replicates</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function automates replacing unquantified values in residue time and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' depth series. For time series, the function performs part of the residue</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' processing proposed in the FOCUS kinetics guidance for parent compounds</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and metabolites. For two-dimensional residue series over time and depth,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' it automates the proposal of Boesten et al (2015).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param res_raw Character vector of a residue time series, or matrix of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' residue values with rows representing depth profiles for a specific sampling</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' time, and columns representing time series of residues at the same depth.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Values below the limit of detection (lod) have to be coded as "nd", values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' between the limit of detection and the limit of quantification, if any, have</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to be coded as "nq". Samples not analysed have to be coded as "na". All</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' values that are not "na", "nd" or "nq" have to be coercible to numeric</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lod Limit of detection (numeric)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param loq Limit of quantification(numeric). Must be specified if the FOCUS rule to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' stop after the first non-detection is to be applied</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param time_zero_presence Do we assume that residues occur at time zero?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This only affects samples from the first sampling time that have been</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' reported as "nd" (not detected).</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' J. and Pol, J. W. (2015). Leaching of plant protection products and their</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformation products; Proposals for improving the assessment of leaching</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to groundwater in the Netherlands — Version 2. Alterra report 2630, Alterra</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Wageningen UR (University & Research centre)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Version 1.1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 18 December 2014, p. 251</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A numeric vector, if a vector was supplied, or a numeric matrix otherwise</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # FOCUS (2014) p. 75/76 and 131/132</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent_1 <- c(.12, .09, .05, .03, "nd", "nd", "nd", "nd", "nd", "nd")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(parent_1, 0.02)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent_2 <- c(.12, .09, .05, .03, "nd", "nd", .03, "nd", "nd", "nd")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(parent_2, 0.02)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq_focus(parent_2, 0.02, loq = 0.05)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent_3 <- c(.12, .09, .05, .03, "nd", "nd", .06, "nd", "nd", "nd")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(parent_3, 0.02)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq_focus(parent_3, 0.02, loq = 0.05)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' metabolite <- c("nd", "nd", "nd", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, "nd", "nd")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(metabolite, 0.02)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq_focus(metabolite, 0.02, 0.05)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Boesten et al. (2015), p. 57/58</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' table_8 <- matrix(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(10, 10, rep("nd", 4),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 10, 10, rep("nq", 2), rep("nd", 2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 10, 10, 10, "nq", "nd", "nd",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "nq", 10, "nq", rep("nd", 3),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "nd", "nq", "nq", rep("nd", 3),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rep("nd", 6), rep("nd", 6)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ncol = 6, byrow = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' table_10 <- matrix(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(10, 10, rep("nd", 4),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 10, 10, rep("nd", 4),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 10, 10, 10, rep("nd", 3),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "nd", 10, rep("nd", 4),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' rep("nd", 18)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ncol = 6, byrow = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set_nd_nq(table_10, 0.5, time_zero_presence = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">set_nd_nq <- function(res_raw, lod, loq = NA, time_zero_presence = FALSE) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.character(res_raw)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">66</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please supply a vector or a matrix of character values")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">68</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.vector(res_raw)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> was_vector <- TRUE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">70</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw <- as.matrix(res_raw)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> was_vector <- FALSE</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.matrix(res_raw)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">74</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Please supply a vector or a matrix of character values")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nq <- 0.5 * (loq + lod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">78</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nda <- 0.5 * lod # not detected but adjacent to detection</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw[res_raw == "nq"] <- nq</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">81</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!time_zero_presence) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (j in 1:ncol(res_raw)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">83</td> + <td class="coverage">3<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (res_raw[1, j] == "nd") res_raw[1, j] <- "na"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw[res_raw == "na"] <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> not_nd_na <- function(value) !(grepl("nd", value) | is.na(value))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:nrow(res_raw)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">94<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (j in 1:ncol(res_raw)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">164<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(res_raw[i, j]) && res_raw[i, j] == "nd") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">98<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (i > 1) { # check earlier sample in same layer</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">17<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (not_nd_na(res_raw[i - 1, j])) res_raw[i, j] <- "nda"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">96</td> + <td class="coverage">98<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (i < nrow(res_raw)) { # check later sample</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">97</td> + <td class="coverage">7<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (not_nd_na(res_raw[i + 1, j])) res_raw[i, j] <- "nda"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">99</td> + <td class="coverage">98<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (j > 1) { # check above sample at the same time</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">9<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (not_nd_na(res_raw[i, j - 1])) res_raw[i, j] <- "nda"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">98<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (j < ncol(res_raw)) { # check sample below at the same time</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (not_nd_na(res_raw[i, j + 1])) res_raw[i, j] <- "nda"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">107</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw[res_raw == "nda"] <- nda</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw[res_raw == "nd"] <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- as.numeric(res_raw)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">112</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(result) <- dim(res_raw)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">113</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames(result) <- dimnames(res_raw)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">114</td> + <td class="coverage">8<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (was_vector) result <- as.vector(result)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">10<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @describeIn set_nd_nq Set non-detects in residue time series according to FOCUS rules</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param set_first_sample_nd Should the first sample be set to "first_sample_nd_value"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in case it is a non-detection?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param first_sample_nd_value Value to be used for the first sample if it is a non-detection</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param ignore_below_loq_after_first_nd Should we ignore values below the LOQ after the first</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' non-detection that occurs after the quantified values?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">set_nd_nq_focus <- function(res_raw, lod, loq = NA,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> set_first_sample_nd = TRUE, first_sample_nd_value = 0,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ignore_below_loq_after_first_nd = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">129</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="missed"> + <td class="num">130</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.vector(res_raw)) stop("FOCUS rules are only specified for one-dimensional time series")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">132</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ignore_below_loq_after_first_nd & is.na(loq)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("You need to specify an LOQ")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n <- length(res_raw)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (ignore_below_loq_after_first_nd) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 3:n) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">35<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!res_raw[i - 2] %in% c("na", "nd")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">21<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (res_raw[i - 1] == "nd") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_remaining <- res_raw[i:n]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_remaining_unquantified <- ifelse(res_remaining == "na", TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(res_remaining == "nd", TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(res_remaining == "nq", TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(suppressWarnings(as.numeric(res_remaining)) < loq, TRUE, FALSE))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">146</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_remaining_numeric <- suppressWarnings(as.numeric(res_remaining))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">147</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_remaining_below_loq <- ifelse(res_remaining == "nq", TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">148</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ifelse(!is.na(res_remaining_numeric) & res_remaining_numeric < loq, TRUE, FALSE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">5<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (all(res_remaining_unquantified)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> res_raw[i:n] <- ifelse(res_remaining_below_loq, "nd", res_remaining)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> result <- set_nd_nq(res_raw, lod = lod, loq = loq)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (set_first_sample_nd) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (res_raw[1] == "nd") result[1] <- first_sample_nd_value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">163</td> + <td class="coverage">4<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(result)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinparplot.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function to plot the confidence intervals obtained using mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function plots the confidence intervals for the parameters fitted using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A fit represented in an \code{\link{mkinfit}} object.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Nothing is returned by this function, as it is called for its side</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' effect, namely to produce a plot.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' phenol = mkinsub("SFO", to = c("anisole")),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anisole = mkinsub("SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinparplot(fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinparplot <- function(object) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">22</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.optim = rownames(subset(object$start, type == "state"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">23</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> deparms.optim = rownames(subset(object$start, type == "deparm"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fractions.optim = grep("^f_", deparms.optim, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N.optim = grep("^N_", deparms.optim, value = TRUE)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">26</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if ("g" %in% deparms.optim) fractions.optim <- c("g", fractions.optim)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rates.optim.unsorted = setdiff(deparms.optim, union(fractions.optim, N.optim))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rates.optim <- rownames(object$start[rates.optim.unsorted, ])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.plot <- c(state.optim = length(state.optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rates.optim = length(rates.optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N.optim = length(N.optim),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fractions.optim = length(fractions.optim))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n.plot <- n.plot[n.plot > 0]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">35</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">36</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">37</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> layout(matrix(1:length(n.plot), ncol = 1), heights = n.plot + 1)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> s <- summary(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpar <- data.frame(t(s$bpar[, c("Estimate", "Lower", "Upper")]))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(mar = c(2.1, 2.1, 0.1, 2.1))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(cex = 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">43</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (type in names(n.plot)) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">44</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parnames <- get(type)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">45</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> values <- bpar[parnames]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">46</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> values_with_confints <- data.frame(t(subset(data.frame(t(values)), !is.na("Lower"))))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">47</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = switch(type,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">48</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> state.optim = range(c(0, unlist(values)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">49</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na.rm = TRUE, finite = TRUE),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">50</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rates.optim = range(c(0, unlist(values)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">51</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na.rm = TRUE, finite = TRUE),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">52</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> N.optim = range(c(0, 1, unlist(values)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na.rm = TRUE, finite = TRUE),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">54</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> fractions.optim = range(c(0, 1, unlist(values)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">55</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> na.rm = TRUE, finite = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">56</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parname_index <- length(parnames):1 # Reverse order for strip chart</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">58</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stripchart(values["Estimate", ][parname_index],</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">59</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlim = xlim,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">60</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylim = c(0.5, length(get(type)) + 0.5),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">61</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> yaxt = "n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">62</td> + <td class="coverage">70<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (type %in% c("rates.optim", "fractions.optim")) abline(v = 0, lty = 2)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">63</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (type %in% c("N.optim", "fractions.optim")) abline(v = 1, lty = 2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">64</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> position <- ifelse(values["Estimate", ] < mean(xlim), "right", "left")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">65</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> text(ifelse(position == "left", min(xlim), max(xlim)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">66</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parname_index, parnames,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">67</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pos = ifelse(position == "left", 4, 2))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">69</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> values.upper.nonInf <- ifelse(values["Upper", ] == Inf, 1.5 * xlim[[2]], values["Upper", ])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Suppress warnings for non-existing arrow lengths</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> suppressWarnings(arrows(as.numeric(values["Lower", ]), parname_index,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">72</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> as.numeric(values.upper.nonInf), parname_index,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">73</td> + <td class="coverage">140<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> code = 3, angle = 90, length = 0.05))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/summary.saem.mmkin.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Summary method for class "saem.mmkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Lists model equations, initial parameter values, optimised parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for fixed effects (population), random effects (deviations from the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' population mean) and residual error model, as well as the resulting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints such as formation fractions and DT50 values. Optionally</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' (default is FALSE), the data are listed in full.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object an object of class [saem.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param x an object of class [summary.saem.mmkin]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param data logical, indicating whether the full data should be included in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param verbose Should the summary be verbose?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param distimes logical, indicating whether DT50 and DT90 values should be</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' included.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits Number of digits to use for printing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots optional arguments passed to methods like \code{print}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inheritParams endpoints</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The summary function returns a list based on the [saemix::SaemixObject]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' obtained in the fit, with at least the following additional components</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{saemixversion, mkinversion, Rversion}{The saemix, mkin and R versions used}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{date.fit, date.summary}{The dates where the fit and the summary were</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' produced}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{diffs}{The differential equations used in the degradation model}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{use_of_ff}{Was maximum or minimum use made of formation fractions}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{data}{The data}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{confint_back}{Backtransformed parameters, with confidence intervals if available}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{confint_errmod}{Error model parameters with confidence intervals}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{ff}{The estimated formation fractions derived from the fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{distimes}{The DT50 and DT90 values for each observed variable.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The print method is called for its side effect, i.e. printing the summary.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats predict vcov</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke for the mkin specific parts</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' saemix authors for the parts inherited from saemix.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Generate five datasets following DFOP-SFO kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO"), quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(1234)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k1_in <- rlnorm(5, log(0.1), 0.3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k2_in <- rlnorm(5, log(0.02), 0.3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' g_in <- plogis(rnorm(5, qlogis(0.5), 0.3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k_m1_in <- rlnorm(5, log(0.02), 0.3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_mean_dfop_sfo <- lapply(1:5, function(i) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkinpredict(dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i],</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, m1 = 0),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(ds_mean_dfop_sfo) <- paste("ds", 1:5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' add_err(ds,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n = 1)[[1]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' })</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Evaluate using mmkin and saem</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE, error_model = "tc", cores = 5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(f_saem_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_dfop_sfo)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' no_random_effect = c("parent_0", "log_k_m1"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' illparms(f_saem_dfop_sfo_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' intervals(f_saem_dfop_sfo_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(f_saem_dfop_sfo_2, data = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Add a correlation between random effects of g and k2</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cov_model_3 <- f_saem_dfop_sfo_2$so@model@covariance.model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cov_model_3["log_k2", "g_qlogis"] <- 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' cov_model_3["g_qlogis", "log_k2"] <- 1</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_saem_dfop_sfo_3 <- update(f_saem_dfop_sfo,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' covariance.model = cov_model_3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' intervals(f_saem_dfop_sfo_3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The correlation does not improve the fit judged by AIC and BIC, although</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # the likelihood is higher with the additional parameter</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova(f_saem_dfop_sfo, f_saem_dfop_sfo_2, f_saem_dfop_sfo_3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">summary.saem.mmkin <- function(object, data = FALSE, verbose = FALSE,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> covariates = NULL, covariate_quantile = 0.5,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> distimes = TRUE, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mod_vars <- names(object$mkinmod$diffs)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> pnames <- names(object$mean_dp_start)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names_fixed_effects <- object$so@results@name.fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_fixed <- length(names_fixed_effects)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> conf.int <- object$so@results@conf.int</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> rownames(conf.int) <- conf.int$name</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_trans <- as.matrix(parms(object, ci = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">110</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(confint_trans)[1] <- "est."</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # In case objects were produced by earlier versions of saem</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">113</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (is.null(object$transformations)) object$transformations <- "mkin"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">115</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (object$transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">116</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bp <- backtransform_odeparms(confint_trans[pnames, "est."], object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">117</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates, object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">118</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpnames <- names(bp)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Transform boundaries of CI for one parameter at a time,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # with the exception of sets of formation fractions (single fractions are OK).</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">122</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names_skip <- character(0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">123</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (box in mod_vars) { # Figure out sets of fractions to skip</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">124</td> + <td class="coverage">492<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> f_names <- grep(paste("^f", box, sep = "_"), pnames, value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">125</td> + <td class="coverage">492<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n_paths <- length(f_names)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">126</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back <- matrix(NA, nrow = length(bp), ncol = 3,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dimnames = list(bpnames, colnames(confint_trans)))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">131</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[, "est."] <- bp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">133</td> + <td class="coverage">396<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (pname in pnames) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">134</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!pname %in% f_names_skip) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">135</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.lower <- confint_trans[pname, "lower"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">136</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par.upper <- confint_trans[pname, "upper"]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">137</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(par.lower) <- names(par.upper) <- pname</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">138</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpl <- backtransform_odeparms(par.lower, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">139</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">140</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">141</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> bpu <- backtransform_odeparms(par.upper, object$mkinmod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">142</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_rates,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">143</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$transform_fractions)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">144</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpl), "lower"] <- bpl</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">145</td> + <td class="coverage">1291<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back[names(bpu), "upper"] <- bpu</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">149</td> + <td class="coverage">404<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_back <- confint_trans[names_fixed_effects, ]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">150</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">151</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">152</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Correlation of fixed effects (inspired by summary.nlme)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">153</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cov_so <- try(solve(object$so@results@fim), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">154</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(cov_so, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">155</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object$corFixed <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">157</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> varFix <- cov_so[1:n_fixed, 1:n_fixed]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">158</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stdFix <- sqrt(diag(varFix))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">159</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$corFixed <- array(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">160</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> t(varFix/stdFix)/stdFix,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">161</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> dim(varFix),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">162</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> list(names_fixed_effects, names_fixed_effects))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Random effects</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">166</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sdnames <- intersect(rownames(conf.int), paste0("SD.", pnames))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">167</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> corrnames <- grep("^Corr.", rownames(conf.int), value = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">168</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_ranef <- as.matrix(conf.int[c(sdnames, corrnames), c("estimate", "lower", "upper")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">169</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(confint_ranef)[1] <- "est."</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Error model</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">172</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> enames <- if (object$err_mod == "const") "a.1" else c("a.1", "b.1")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">173</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> confint_errmod <- as.matrix(conf.int[enames, c("estimate", "lower", "upper")])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">174</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames(confint_errmod)[1] <- "est."</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">176</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_trans <- confint_trans</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_ranef <- confint_ranef</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_errmod <- confint_errmod</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$confint_back <- confint_back</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$date.summary = date()</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$use_of_ff = object$mkinmod$use_of_ff</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$error_model_algorithm = object$mmkin_orig[[1]]$error_model_algorithm</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">184</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> err_mod = object$mmkin_orig[[1]]$err_mod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">186</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$diffs <- object$mkinmod$diffs</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">187</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$print_data <- data # boolean: Should we print the data?</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">188</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> so_pred <- object$so@results@predictions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">190</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(object$data)[4] <- "observed" # rename value to observed</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">192</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$verbose <- verbose</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">194</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$fixed <- object$mmkin_orig[[1]]$fixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">195</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll <-try(logLik(object$so, method = "is"), silent = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">196</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(ll, "try-error")) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">197</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object$logLik <- object$AIC <- object $BIC <- NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">199</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$logLik = logLik(object$so, method = "is")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">200</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$AIC = AIC(object$so)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">201</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$BIC = BIC(object$so)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">204</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ep <- endpoints(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">205</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$covariates <- ep$covariates</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">206</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$ff) != 0)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">207</td> + <td class="coverage">330<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object$ff <- ep$ff</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">208</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (distimes) object$distimes <- ep$distimes</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">209</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(ep$SFORB) != 0) object$SFORB <- ep$SFORB</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">210</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(object) <- c("summary.saem.mmkin")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">211</td> + <td class="coverage">800<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(object)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname summary.saem.mmkin</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">print.summary.saem.mmkin <- function(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">217</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("saemix version used for fitting: ", x$saemixversion, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">218</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("mkin version used for pre-fitting: ", x$mkinversion, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">219</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("R version used for fitting: ", x$Rversion, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">221</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of fit: ", x$date.fit, "\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">222</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Date of summary:", x$date.summary, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">223</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">224</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEquations:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">225</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> nice_diffs <- gsub("^(d.*) =", "\\1/dt =", x[["diffs"]])</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">226</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> writeLines(strwrap(nice_diffs, exdent = 11))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">228</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">229</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(nrow(x$data), "observations of",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">230</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$name)), "variable(s) grouped in",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">231</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> length(unique(x$data$ds)), "datasets\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">233</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nModel predictions using solution type", x$solution_type, "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">235</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFitted in", x$time[["elapsed"]], "s\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">236</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Using", paste(x$so@options$nbiter.saemix, collapse = ", "),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> "iterations and", x$so@options$nb.chains, "chains\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">239</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nVariance model: ")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">240</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat(switch(x$err_mod,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">241</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> const = "Constant variance",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">242</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> obs = "Variance unique to each observed variable",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">243</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> tc = "Two-component variance function"), "\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">244</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">245</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStarting values for degradation parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">246</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$mean_dp_start, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">247</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">248</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nFixed degradation parameter values:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">249</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(length(x$fixed$value) == 0) cat("None\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">250</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> else print(x$fixed, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">251</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">252</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStarting values for random effects (square root of initial entries in omega):\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">253</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(sqrt(x$so@model@omega.init), digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">254</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">255</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nStarting values for error model parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">256</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- x$so@model@error.init</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">257</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(errparms) <- x$so@model@name.sigma</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">258</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> errparms <- errparms[x$so@model@indx.res]</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">259</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(errparms, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">260</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">261</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResults:\n\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">262</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("Likelihood computed by importance sampling\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">263</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(AIC = x$AIC, BIC = x$BIC, logLik = x$logLik,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">264</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = " "), digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">265</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">266</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nOptimised parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">267</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_trans, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">268</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">269</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (identical(x$corFixed, NA)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">270</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nCorrelation is not available\n")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">271</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">272</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> corr <- x$corFixed</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">273</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(corr) <- "correlation"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">274</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(corr, title = "\nCorrelation:", rdig = digits, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">275</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">276</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">277</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nRandom effects:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">278</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_ranef, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">279</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">280</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nVariance model:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">281</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_errmod, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">282</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">283</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (x$transformations == "mkin") {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">284</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nBacktransformed parameters:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">285</td> + <td class="coverage">125<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$confint_back, digits = digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">286</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">287</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">288</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.null(x$covariates)) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">289</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nCovariates used for endpoints below:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">290</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$covariates)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">291</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">292</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">293</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printSFORB <- !is.null(x$SFORB)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">294</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printSFORB){</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">295</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated Eigenvalues of SFORB model(s):\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">296</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$SFORB, digits = digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">297</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">298</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">299</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printff <- !is.null(x$ff)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">300</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printff){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">301</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nResulting formation fractions:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">302</td> + <td class="coverage">117<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(data.frame(ff = x$ff), digits = digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">303</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">304</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">305</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> printdistimes <- !is.null(x$distimes)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">306</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if(printdistimes){</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">307</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nEstimated disappearance times:\n")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">308</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> print(x$distimes, digits = digits,...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">309</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">310</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">311</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (x$print_data){</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">312</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> cat("\nData:\n")</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">313</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> print(format(x$data, digits = digits, ...), row.names = FALSE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">314</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">315</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">316</td> + <td class="coverage">242<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> invisible(x)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">317</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkin_long_to_wide.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Convert a dataframe from long to wide format</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function takes a dataframe in the long form, i.e. with a row for each</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed value, and converts it into a dataframe with one independent</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' variable and several dependent variables as columns.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param long_data The dataframe must contain one variable called "time" with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the time values specified by the \code{time} argument, one column called</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' "name" with the grouping of the observed values, and finally one column of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed values called "value".</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param time The name of the time variable in the long input data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param outtime The name of the time variable in the wide output data.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Dataframe in wide format.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkin_long_to_wide(FOCUS_2006_D)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export mkin_long_to_wide</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkin_long_to_wide <- function(long_data, time = "time", outtime = "time")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">22</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames <- unique(long_data$name)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">23</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> wide_data <- data.frame(time = subset(long_data, name == colnames[1], time))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> names(wide_data) <- outtime</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (var in colnames) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">26</td> + <td class="coverage">741<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> wide_data[var] <- subset(long_data, name == var, value)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">494<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(wide_data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/loftest.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Lack-of-fit test for models fitted to data with replicates</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This is a generic function with a method currently only defined for mkinfit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' objects. It fits an anova model to the data contained in the object and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' compares the likelihoods using the likelihood ratio test</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link[lmtest]{lrtest.default}} from the lmtest package.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The anova model is interpreted as the simplest form of an mkinfit model,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' assuming only a constant variance about the means, but not enforcing any</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' structure of the means, so we have one model parameter for every mean</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' of replicate samples.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object A model object with a defined loftest method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Not used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">loftest <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">17</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> UseMethod("loftest")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname loftest</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats logLik lm dnorm coef</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso lrtest</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == "parent")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_fit <- mkinfit("SFO", test_data, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(sfo_fit) # We see a clear pattern in the residuals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loftest(sfo_fit) # We have a clear lack of fit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We try a different model (the one that was used to generate the data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_fit <- mkinfit("DFOP", test_data, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(dfop_fit) # We don't see systematic deviations, but heteroscedastic residuals</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # therefore we should consider adapting the error model, although we have</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loftest(dfop_fit) # no lack of fit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This is the anova model used internally for the comparison</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_anova <- test_data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_anova$time <- as.factor(test_data_anova$time)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova_fit <- lm(value ~ time, data = test_data_anova)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(anova_fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' logLik(anova_fit) # We get the same likelihood and degrees of freedom</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_2 <- synthetic_data_for_UBA_2014[[12]]$data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = list(type = "SFO", to = "M2"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = list(type = "SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_lin_fit <- mkinfit(m_synth_SFO_lin, test_data_2, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(sfo_lin_fit) # not a good model, we try parallel formation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loftest(sfo_lin_fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2")),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = list(type = "SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = list(type = "SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_par_fit <- mkinfit(m_synth_SFO_par, test_data_2, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(sfo_par_fit) # much better for metabolites</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loftest(sfo_par_fit)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2")),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = list(type = "SFO"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M2 = list(type = "SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dfop_par_fit <- mkinfit(m_synth_DFOP_par, test_data_2, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(dfop_par_fit) # No visual lack of fit</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' loftest(dfop_par_fit) # no lack of fit found by the test</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' #</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The anova model used for comparison in the case of transformation products</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_anova_2 <- dfop_par_fit$data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_anova_2$variable <- as.factor(test_data_anova_2$variable)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' test_data_anova_2$time <- as.factor(test_data_anova_2$time)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' anova_fit_2 <- lm(observed ~ time:variable - 1, data = test_data_anova_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(anova_fit_2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">loftest.mkinfit <- function(object, ...) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">75</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name_function <- function(x) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">76</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_name <- paste(x$mkinmod$name, "with error model", x$err_mod)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (length(x$bparms.fixed) > 0) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">78</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object_name <- paste(object_name,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">79</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> "and fixed parameter(s)",</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">80</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> paste(names(x$bparms.fixed), collapse = ", "))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(object_name)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Check if we have replicates in the data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">86</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (max(aggregate(object$data$observed,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">87</td> + <td class="coverage">2<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> by = list(object$data$variable, object$data$time), length)$x) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> stop("Not defined for fits to data without replicates")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">91</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_anova <- object$data</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_anova$time <- as.factor(data_anova$time)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">93</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> data_anova$variable <- as.factor(data_anova$variable)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">94</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (nlevels(data_anova$variable) == 1) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2 <- lm(observed ~ time - 1, data = data_anova)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">97</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> object_2 <- lm(observed ~ variable:time - 1,</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">98</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> data = data_anova)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">101</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$mkinmod <- list(name = "ANOVA")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">102</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$err_mod <- "const"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sigma_mle <- sqrt(sum(residuals(object_2)^2)/nobs(object_2))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">104</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$logLik <- sum(dnorm(x = object_2$residuals,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">105</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> mean = 0, sd = sigma_mle, log = TRUE))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">106</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$data <- object$data # to make the nobs.mkinfit method work</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$bparms.optim <- coef(object_2)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">108</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> object_2$errparms <- 1 # We have estimated one error model parameter</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">109</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(object_2) <- "mkinfit"</pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">111</td> + <td class="coverage">1<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lmtest::lrtest.default(object_2, object, name = name_function)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/add_err.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Add normally distributed errors to simulated kinetic degradation data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Normally distributed errors are added to data predicted for a specific</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' degradation model using \code{\link{mkinpredict}}. The variance of the error</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' may depend on the predicted value and is specified as a standard deviation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param prediction A prediction from a kinetic model as produced by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinpredict}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param sdfunc A function taking the predicted value as its only argument and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' returning a standard deviation that should be used for generating the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' random error terms for this value.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param secondary The names of state variables that should have an initial</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' value of zero</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param n The number of datasets to be generated.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param LOD The limit of detection (LOD). Values that are below the LOD after</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' adding the random error will be set to NA.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param reps The number of replicates to be generated within the datasets.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param digits The number of digits to which the values will be rounded.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param seed The seed used for the generation of random numbers. If NA, the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' seed is not set.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats rnorm</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list of datasets compatible with \code{\link{mmkin}}, i.e. the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' components of the list are datasets compatible with \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Ranke J and Lehmann R (2015) To t-test or not to t-test, that is</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the question. XV Symposium on Pesticide Chemistry 2-4 September 2015,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Piacenza, Italy</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' https://jrwb.de/posters/piacenza_2015.pdf</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # The kinetic model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' M1 = mkinsub("SFO"), use_of_ff = "max")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Generate a prediction for a specific set of parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # This is the prediction used for the "Type 2 datasets" on the Piacenza poster</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # from 2015</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_SFO <- mkinpredict(m_SFO_SFO,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(k_parent = 0.1, f_parent_to_M1 = 0.5,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' k_M1 = log(2)/1000),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' c(parent = 100, M1 = 0),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Add an error term with a constant (independent of the value) standard deviation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # of 10, and generate three datasets</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Name the datasets for nicer plotting</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' names(d_SFO_SFO_err) <- paste("Dataset", 1:3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Name the model in the list of models (with only one member in this case) for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # nicer plotting later on. Be quiet and use only one core not to offend CRAN</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # checks</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_SFO_SFO_err, cores = 1,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_SFO_SFO)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # We would like to inspect the fit for dataset 3 more closely</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Using double brackets makes the returned object an mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # instead of a list of mkinfit objects, so plot.mkinfit is used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_SFO_SFO[[3]], show_residuals = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # If we use single brackets, we should give two indices (model and dataset),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # and plot.mmkin is used</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(f_SFO_SFO[1, 3])</pre> + </td> + </tr> + <tr class="never"> + <td class="num">71</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">add_err <- function(prediction, sdfunc, secondary = c("M1", "M2"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> n = 10, LOD = 0.1, reps = 2, digits = 1, seed = NA)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">77</td> + <td class="coverage">842<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (!is.na(seed)) set.seed(seed)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">79</td> + <td class="coverage">862<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> prediction <- as.data.frame(prediction)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # The output of mkinpredict is in wide format</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">82</td> + <td class="coverage">862<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_long = mkin_wide_to_long(prediction, time = "time")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set up the list to be returned</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">85</td> + <td class="coverage">862<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_return = list()</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Generate datasets one by one in a loop</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">88</td> + <td class="coverage">862<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> for (i in 1:n) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">89</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_rep = data.frame(lapply(d_long, rep, each = reps))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">90</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">92</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_rep[d_rep$time == 0 & d_rep$name %in% secondary, "value"] <- 0</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Set values below the LOD to NA</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">95</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Round the values for convenience</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">98</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_NA$value <- round(d_NA$value, digits)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">100</td> + <td class="coverage">1712<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> d_return[[i]] <- d_NA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">103</td> + <td class="coverage">862<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(d_return)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkin_wide_to_long.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">utils::globalVariables(c("name", "time", "value"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Convert a dataframe with observations over time into long format</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function simply takes a dataframe with one independent variable and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' several dependent variable and converts it into the long form as required by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param wide_data The dataframe must contain one variable with the time</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' values specified by the \code{time} argument and usually more than one</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' column of observed values.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param time The name of the time variable.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return Dataframe in long format as needed for \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @keywords manip</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' mkin_wide_to_long(wide)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' </pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkin_wide_to_long <- function(wide_data, time = "t")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">24</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> wide_data <- as.data.frame(wide_data)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">25</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> colnames <- names(wide_data)</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">26</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (!(time %in% colnames)) stop("The data in wide format have to contain a variable named ", time, ".")</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">27</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> vars <- subset(colnames, colnames != time)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> n <- length(colnames) - 1</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> long_data <- data.frame(</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">30</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> name = rep(vars, each = length(wide_data[[time]])),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> time = as.numeric(rep(wide_data[[time]], n)),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> value = as.numeric(unlist(wide_data[vars])),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> row.names = NULL)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">1127<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(long_data)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/parent_solutions.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Single First-Order kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing exponential decline from a defined starting value.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param t Time.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param parent_0 Starting value for the response variable at time zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k Kinetic rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The value of the response variable at time \code{t}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Version 1.1, 18 December 2014</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{plot(function(x) SFO.solution(x, 100, 3), 0, 2)}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">SFO.solution <- function(t, parent_0, k)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">2338849<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = parent_0 * exp(-k * t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' First-Order Multi-Compartment kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing exponential decline from a defined starting value, with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a decreasing rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The form given here differs slightly from the original reference by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Gustafson and Holden (1990). The parameter \code{beta} corresponds to 1/beta</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' in the original equation.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit SFO.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param alpha Shape parameter determined by coefficient of variation of rate</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' constant values.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param beta Location parameter.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note The solution of the FOMC kinetic model reduces to the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{SFO.solution}} for large values of \code{alpha} and \code{beta}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">53</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">55</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence</pre> + </td> + </tr> + <tr class="never"> + <td class="num">56</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and Degradation Kinetics from Environmental Fate Studies on Pesticides in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">57</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">58</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Version 1.1, 18 December 2014</pre> + </td> + </tr> + <tr class="never"> + <td class="num">59</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">60</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">61</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil:</pre> + </td> + </tr> + <tr class="never"> + <td class="num">62</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' A new model based on spatial variability. \emph{Environmental Science and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">63</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Technology} \bold{24}, 1032-1038</pre> + </td> + </tr> + <tr class="never"> + <td class="num">64</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">65</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">66</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">67</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">68</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">69</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">FOMC.solution <- function(t, parent_0, alpha, beta)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">70</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">71</td> + <td class="coverage">32626<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = parent_0 / (t/beta + 1)^alpha</pre> + </td> + </tr> + <tr class="never"> + <td class="num">72</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">73</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">74</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Indeterminate order rate equation kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">75</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">76</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing exponential decline from a defined starting value, with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">77</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' a concentration dependent rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">78</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">79</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">80</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit SFO.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">81</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k__iore Rate constant. Note that this depends on the concentration</pre> + </td> + </tr> + <tr class="never"> + <td class="num">82</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' units used.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">83</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param N Exponent describing the nonlinearity of the rate equation</pre> + </td> + </tr> + <tr class="never"> + <td class="num">84</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note The solution of the IORE kinetic model reduces to the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">85</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can</pre> + </td> + </tr> + <tr class="never"> + <td class="num">86</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' be transformed to equivalent parameters of the FOMC mode - see the NAFTA</pre> + </td> + </tr> + <tr class="never"> + <td class="num">87</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' guidance for details.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">88</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references NAFTA Technical Working Group on Pesticides (not dated) Guidance</pre> + </td> + </tr> + <tr class="never"> + <td class="num">89</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' for Evaluating and Calculating Degradation Kinetics in Environmental Media</pre> + </td> + </tr> + <tr class="never"> + <td class="num">90</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">91</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">92</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">93</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">94</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.fomc <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">95</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.iore <- mkinfit("IORE", FOCUS_2006_C, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">96</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fit.iore.deS <- mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">97</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">98</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">99</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' row.names = paste("model par", 1:4)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">100</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">101</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' iore.deS = endpoints(fit.iore)$distimes))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">102</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">103</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">104</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">105</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">IORE.solution <- function(t, parent_0, k__iore, N)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">106</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">107</td> + <td class="coverage">42328<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = (parent_0^(1 - N) - (1 - N) * k__iore * t)^(1/(1 - N))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">108</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">109</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">110</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Double First-Order in Parallel kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">111</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">112</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing decline from a defined starting value using the sum of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">113</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' two exponential decline functions.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">114</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">115</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">116</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit SFO.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">117</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param t Time.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">118</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k1 First kinetic constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">119</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k2 Second kinetic constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">120</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param g Fraction of the starting value declining according to the first</pre> + </td> + </tr> + <tr class="never"> + <td class="num">121</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' kinetic constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">122</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">123</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">124</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim = c(0,100))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">125</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">126</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">127</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">DFOP.solution <- function(t, parent_0, k1, k2, g)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">128</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">129</td> + <td class="coverage">1904176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = g * parent_0 * exp(-k1 * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">130</td> + <td class="coverage">1904176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (1 - g) * parent_0 * exp(-k2 * t)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">131</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">132</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">133</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Hockey-Stick kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">134</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">135</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing two exponential decline functions with a break point</pre> + </td> + </tr> + <tr class="never"> + <td class="num">136</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' between them.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">137</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">138</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">139</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit DFOP.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">140</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param tb Break point. Before this time, exponential decline according to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">141</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{k1} is calculated, after this time, exponential decline proceeds</pre> + </td> + </tr> + <tr class="never"> + <td class="num">142</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' according to \code{k2}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">143</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">144</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">145</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">146</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">147</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">148</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">HS.solution <- function(t, parent_0, k1, k2, tb)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">149</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">150</td> + <td class="coverage">22552<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = ifelse(t <= tb,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">151</td> + <td class="coverage">22552<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_0 * exp(-k1 * t),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">152</td> + <td class="coverage">22552<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent_0 * exp(-k1 * tb) * exp(-k2 * (t - tb)))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">153</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">154</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">155</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Single First-Order Reversible Binding kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">156</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">157</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing the solution of the differential equations describing</pre> + </td> + </tr> + <tr class="never"> + <td class="num">158</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the kinetic model with first-order terms for a two-way transfer from a free</pre> + </td> + </tr> + <tr class="never"> + <td class="num">159</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' to a bound fraction, and a first-order degradation term for the free</pre> + </td> + </tr> + <tr class="never"> + <td class="num">160</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fraction. The initial condition is a defined amount in the free fraction</pre> + </td> + </tr> + <tr class="never"> + <td class="num">161</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and no substance in the bound fraction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">162</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">163</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">164</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit SFO.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">165</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k_12 Kinetic constant describing transfer from free to bound.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">166</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k_21 Kinetic constant describing transfer from bound to free.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">167</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k_1output Kinetic constant describing degradation of the free</pre> + </td> + </tr> + <tr class="never"> + <td class="num">168</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' fraction.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">169</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The value of the response variable, which is the sum of free and</pre> + </td> + </tr> + <tr class="never"> + <td class="num">170</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' bound fractions at time \code{t}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">171</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">172</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">173</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">174</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">175</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">176</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">SFORB.solution = function(t, parent_0, k_12, k_21, k_1output) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">177</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - k_1output * k_21)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">178</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">179</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp</pre> + </td> + </tr> + <tr class="never"> + <td class="num">180</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">181</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = parent_0 *</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">182</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">183</td> + <td class="coverage">9240<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">184</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + <tr class="never"> + <td class="num">185</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="never"> + <td class="num">186</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Logistic kinetics</pre> + </td> + </tr> + <tr class="never"> + <td class="num">187</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">188</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing exponential decline from a defined starting value, with</pre> + </td> + </tr> + <tr class="never"> + <td class="num">189</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' an increasing rate constant, supposedly caused by microbial growth</pre> + </td> + </tr> + <tr class="never"> + <td class="num">190</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">191</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @family parent solutions</pre> + </td> + </tr> + <tr class="never"> + <td class="num">192</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @inherit SFO.solution</pre> + </td> + </tr> + <tr class="never"> + <td class="num">193</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param kmax Maximum rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">194</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param k0 Minimum rate constant effective at time zero.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">195</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param r Growth rate of the increase in the rate constant.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">196</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @note The solution of the logistic model reduces to the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">197</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">198</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">199</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">200</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Reproduce the plot on page 57 of FOCUS (2014)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">201</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">202</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from = 0, to = 100, ylim = c(0, 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">203</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' xlab = "Time", ylab = "Residue")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">204</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">205</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from = 0, to = 100, add = TRUE, lty = 2, col = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">206</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">207</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from = 0, to = 100, add = TRUE, lty = 3, col = 3)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">208</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">209</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from = 0, to = 100, add = TRUE, lty = 4, col = 4)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">210</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">211</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' from = 0, to = 100, add = TRUE, lty = 5, col = 5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">212</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' legend("topright", inset = 0.05,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">213</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">214</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">215</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' lty = 1:5, col = 1:5)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">216</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">217</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' # Fit with synthetic data</pre> + </td> + </tr> + <tr class="never"> + <td class="num">218</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' logistic <- mkinmod(parent = mkinsub("logistic"))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">219</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">220</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">221</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">222</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_logistic <- mkinpredict(logistic,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">223</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parms_logistic, c(parent = 100),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">224</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sampling_times)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">225</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_2_1 <- add_err(d_logistic,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">226</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">227</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">228</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">229</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m <- mkinfit("logistic", d_2_1, quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">230</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_sep(m)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">231</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' summary(m)$bpar</pre> + </td> + </tr> + <tr class="never"> + <td class="num">232</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' endpoints(m)$distimes</pre> + </td> + </tr> + <tr class="never"> + <td class="num">233</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">234</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">235</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">logistic.solution <- function(t, parent_0, kmax, k0, r)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">236</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">237</td> + <td class="coverage">56304<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> parent = parent_0 * (kmax / (kmax - k0 + k0 * exp (r * t))) ^(kmax/r)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">238</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/llhist.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Plot the distribution of log likelihoods from multistart objects</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Produces a histogram of log-likelihoods. In addition, the likelihood of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' original fit is shown as a red vertical line.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object The [multistart] object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param breaks Passed to [hist]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param lpos Positioning of the legend.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param main Title of the plot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots Passed to [hist]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso [multistart]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">llhist <- function(object, breaks = "Sturges", lpos = "topleft", main = "",</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">16</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> oldpar <- par(no.readonly = TRUE)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">17</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> on.exit(par(oldpar, no.readonly = TRUE))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">19</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object, "multistart.saem.mmkin")) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">20</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> llfunc <- function(object) {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">21</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> if (inherits(object$so, "try-error")) return(NA)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">22</td> + <td class="coverage">1408<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> else return(logLik(object$so))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> } else {</pre> + </td> + </tr> + <tr class="missed"> + <td class="num">25</td> + <td class="coverage">!</td> + <td class="col-sm-12"> + <pre class="language-r"> stop("llhist is only implemented for multistart.saem.mmkin objects")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">28</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll_orig <- logLik(attr(object, "orig"))</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">29</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ll <- stats::na.omit(sapply(object, llfunc))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">31</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> par(las = 1)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">32</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> h <- hist(ll, freq = TRUE,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">33</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> xlab = "", main = main,</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">34</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> ylab = "Frequency of log likelihoods", breaks = breaks, ...)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">36</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> freq_factor <- h$counts[1] / h$density[1]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">38</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> abline(v = ll_orig, col = 2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"></pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend(lpos, inset = c(0.05, 0.05), bty = "n",</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> lty = 1, col = c(2),</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">176<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> legend = "original fit")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/logLik.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Calculated the log-likelihood of a fitted mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This function returns the product of the likelihood densities of each</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed value, as calculated as part of the fitting procedure using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{dnorm}}, i.e. assuming normal distribution, and with the means</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' predicted by the degradation model, and the standard deviations predicted by</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the error model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' The total number of estimated parameters returned with the value of the</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' likelihood is calculated as the sum of fitted degradation model parameters</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' and the fitted error model parameters.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An object of class \code{\link{mkinfit}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For compatibility with the generic method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return An object of class \code{\link{logLik}} with the number of estimated</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parameters (degradation model parameters plus variance model parameters)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' as attribute.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @author Johannes Ranke</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @seealso Compare the AIC of columns of \code{\link{mmkin}} objects using</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \code{\link{AIC.mmkin}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \dontrun{</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sfo_sfo <- mkinmod(</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' parent = mkinsub("SFO", to = "m1"),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' m1 = mkinsub("SFO")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' )</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_t <- subset(FOCUS_2006_D, value != 0)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_obs <- update(f_nw, error_model = "obs")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_tc <- update(f_nw, error_model = "tc")</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f_nw, f_obs, f_tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">logLik.mkinfit <- function(object, ...) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">37</td> + <td class="coverage">166798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> val <- object$logLik</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r"> # Number of estimated parameters</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">39</td> + <td class="coverage">166798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(val, "df") <- length(object$bparms.optim) + length(object$errparms)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">40</td> + <td class="coverage">166798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> attr(val, "nobs") <- nobs(object)</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">41</td> + <td class="coverage">166798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> class(val) <- "logLik"</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">42</td> + <td class="coverage">166798<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(val)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/nobs.mkinfit.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Number of observations on which an mkinfit object was fitted</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @importFrom stats nobs</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param object An mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param \dots For compatibility with the generic method</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The number of rows in the data included in the mkinfit object</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">8</td> + <td class="coverage">166810<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r">nobs.mkinfit <- function(object, ...) nrow(object$data)</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/sigma_twocomp.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Two-component error model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Function describing the standard deviation of the measurement error in</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' dependence of the measured value \eqn{y}:</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \deqn{\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}} sigma =</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' sqrt(sigma_low^2 + y^2 * rsd_high^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' This is the error model used for example by Werner et al. (1978). The model</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' proposed by Rocke and Lorenzato (1995) can be written in this form as well,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' but assumes approximate lognormal distribution of errors for high values of</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' y.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param y The magnitude of the observed value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param sigma_low The asymptotic minimum of the standard deviation for low</pre> + </td> + </tr> + <tr class="never"> + <td class="num">16</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' observed values</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param rsd_high The coefficient describing the increase of the standard</pre> + </td> + </tr> + <tr class="never"> + <td class="num">18</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' deviation with the magnitude of the observed value</pre> + </td> + </tr> + <tr class="never"> + <td class="num">19</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return The standard deviation of the response variable.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">20</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @references Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">21</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry</pre> + </td> + </tr> + <tr class="never"> + <td class="num">22</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' 24(11), 1895-1898.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">23</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">24</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for</pre> + </td> + </tr> + <tr class="never"> + <td class="num">25</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' measurement error in analytical chemistry. Technometrics 37(2), 176-184.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">26</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">27</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical</pre> + </td> + </tr> + <tr class="never"> + <td class="num">28</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' Degradation Data. *Environments* 6(12) 124</pre> + </td> + </tr> + <tr class="never"> + <td class="num">29</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' \doi{10.3390/environments6120124}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">30</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#'</pre> + </td> + </tr> + <tr class="never"> + <td class="num">31</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @examples</pre> + </td> + </tr> + <tr class="never"> + <td class="num">32</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' times <- c(0, 1, 3, 7, 14, 28, 60, 90, 120)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">33</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_pred <- data.frame(time = times, parent = 100 * exp(- 0.03 * times))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">34</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' set.seed(123456)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">35</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' d_syn <- add_err(d_pred, function(y) sigma_twocomp(y, 1, 0.07),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">36</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' reps = 2, n = 1)[[1]]</pre> + </td> + </tr> + <tr class="never"> + <td class="num">37</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_nls <- nls(value ~ SSasymp(time, 0, parent_0, lrc), data = d_syn,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">38</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' start = list(parent_0 = 100, lrc = -3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">39</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' library(nlme)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">40</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_gnls <- gnls(value ~ SSasymp(time, 0, parent_0, lrc),</pre> + </td> + </tr> + <tr class="never"> + <td class="num">41</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' data = d_syn, na.action = na.omit,</pre> + </td> + </tr> + <tr class="never"> + <td class="num">42</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' start = list(parent_0 = 100, lrc = -3))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">43</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' if (length(findFunction("varConstProp")) > 0) {</pre> + </td> + </tr> + <tr class="never"> + <td class="num">44</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_gnls_tc <- update(f_gnls, weights = varConstProp())</pre> + </td> + </tr> + <tr class="never"> + <td class="num">45</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_gnls_tc_sf <- update(f_gnls_tc, control = list(sigma = 1))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">46</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' }</pre> + </td> + </tr> + <tr class="never"> + <td class="num">47</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mkin <- mkinfit("SFO", d_syn, error_model = "const", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">48</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' f_mkin_tc <- mkinfit("SFO", d_syn, error_model = "tc", quiet = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">49</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' plot_res(f_mkin_tc, standardized = TRUE)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">50</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' AIC(f_nls, f_gnls, f_gnls_tc, f_gnls_tc_sf, f_mkin, f_mkin_tc)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">51</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">52</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">sigma_twocomp <- function(y, sigma_low, rsd_high) {</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">53</td> + <td class="coverage">4250<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> sqrt(sigma_low^2 + y^2 * rsd_high^2)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">54</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <div id="R/mkinsub.R" class="hidden"> + <table class="table-condensed"> + <tbody> + <tr class="never"> + <td class="num">1</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @rdname mkinmod</pre> + </td> + </tr> + <tr class="never"> + <td class="num">2</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param submodel Character vector of length one to specify the submodel type.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">3</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' See \code{\link{mkinmod}} for the list of allowed submodel names.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">4</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param to Vector of the names of the state variable to which a</pre> + </td> + </tr> + <tr class="never"> + <td class="num">5</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' transformation shall be included in the model.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">6</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param sink Should a pathway to sink be included in the model in addition to</pre> + </td> + </tr> + <tr class="never"> + <td class="num">7</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' the pathways to other state variables?</pre> + </td> + </tr> + <tr class="never"> + <td class="num">8</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @param full_name An optional name to be used e.g. for plotting fits</pre> + </td> + </tr> + <tr class="never"> + <td class="num">9</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' performed with the model. You can use non-ASCII characters here, but then</pre> + </td> + </tr> + <tr class="never"> + <td class="num">10</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' your R code will not be portable, \emph{i.e.} may produce unintended plot</pre> + </td> + </tr> + <tr class="never"> + <td class="num">11</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' results on other operating systems or system configurations.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">12</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @return A list for use with \code{\link{mkinmod}}.</pre> + </td> + </tr> + <tr class="never"> + <td class="num">13</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">#' @export</pre> + </td> + </tr> + <tr class="never"> + <td class="num">14</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">mkinsub <- function(submodel, to = NULL, sink = TRUE, full_name = NA)</pre> + </td> + </tr> + <tr class="never"> + <td class="num">15</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">{</pre> + </td> + </tr> + <tr class="covered"> + <td class="num">16</td> + <td class="coverage">9864<em>x</em></td> + <td class="col-sm-12"> + <pre class="language-r"> return(list(type = submodel, to = to, sink = sink, full_name = full_name))</pre> + </td> + </tr> + <tr class="never"> + <td class="num">17</td> + <td class="coverage"></td> + <td class="col-sm-12"> + <pre class="language-r">}</pre> + </td> + </tr> + </tbody> + </table> + </div> + <script>$('div#files pre').each(function(i, block) { + hljs.highlightBlock(block); +});</script> + </div> + </div> + </div> + </div> + </div> +</div> +</body> +</html> diff --git a/docs/coverage/lib/bootstrap-3.3.5/css/bootstrap-theme.min.css b/docs/coverage/lib/bootstrap-3.3.5/css/bootstrap-theme.min.css new 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+}; diff --git a/docs/coverage/lib/crosstalk-1.2.1/css/crosstalk.min.css b/docs/coverage/lib/crosstalk-1.2.1/css/crosstalk.min.css new file mode 100644 index 00000000..6b453828 --- /dev/null +++ b/docs/coverage/lib/crosstalk-1.2.1/css/crosstalk.min.css @@ -0,0 +1 @@ +.container-fluid.crosstalk-bscols{margin-left:-30px;margin-right:-30px;white-space:normal}body>.container-fluid.crosstalk-bscols{margin-left:auto;margin-right:auto}.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:inline-block;padding-right:12px;vertical-align:top}@media only screen and (max-width: 480px){.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column{display:block;padding-right:inherit}}.crosstalk-input{margin-bottom:15px}.crosstalk-input .control-label{margin-bottom:0;vertical-align:middle}.crosstalk-input input[type="checkbox"]{margin:4px 0 0;margin-top:1px;line-height:normal}.crosstalk-input .checkbox{position:relative;display:block;margin-top:10px;margin-bottom:10px}.crosstalk-input .checkbox>label{padding-left:20px;margin-bottom:0;font-weight:400;cursor:pointer}.crosstalk-input .checkbox input[type="checkbox"],.crosstalk-input .checkbox-inline input[type="checkbox"]{position:absolute;margin-top:2px;margin-left:-20px}.crosstalk-input .checkbox+.checkbox{margin-top:-5px}.crosstalk-input .checkbox-inline{position:relative;display:inline-block;padding-left:20px;margin-bottom:0;font-weight:400;vertical-align:middle;cursor:pointer}.crosstalk-input .checkbox-inline+.checkbox-inline{margin-top:0;margin-left:10px} diff --git a/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js new file mode 100644 index 00000000..fd9eb53d --- /dev/null +++ b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js @@ -0,0 +1,1474 @@ +(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()({1:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var Events = function () { + function Events() { + _classCallCheck(this, Events); + + this._types = {}; + this._seq = 0; + } + + _createClass(Events, [{ + key: "on", + value: function on(eventType, listener) { + var subs = this._types[eventType]; + if (!subs) { + subs = this._types[eventType] = {}; + } + var sub = "sub" + this._seq++; + subs[sub] = listener; + return sub; + } + + // Returns false if no match, or string for sub name if matched + + }, { + key: "off", + value: function off(eventType, listener) { + var subs = this._types[eventType]; + if (typeof listener === "function") { + for (var key in subs) { + if (subs.hasOwnProperty(key)) { + if (subs[key] === listener) { + delete subs[key]; + return key; + } + } + } + return false; + } else if (typeof listener === "string") { + if (subs && subs[listener]) { + delete subs[listener]; + return listener; + } + return false; + } else { + throw new Error("Unexpected type for listener"); + } + } + }, { + key: "trigger", + value: function trigger(eventType, arg, thisObj) { + var subs = this._types[eventType]; + for (var key in subs) { + if (subs.hasOwnProperty(key)) { + subs[key].call(thisObj, arg); + } + } + } + }]); + + return Events; +}(); + +exports.default = Events; + +},{}],2:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.FilterHandle = undefined; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +var _filterset = require("./filterset"); + +var _filterset2 = _interopRequireDefault(_filterset); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function getFilterSet(group) { + var fsVar = group.var("filterset"); + var result = fsVar.get(); + if (!result) { + result = new _filterset2.default(); + fsVar.set(result); + } + return result; +} + +var id = 1; +function nextId() { + return id++; +} + +/** + * Use this class to contribute to, and listen for changes to, the filter set + * for the given group of widgets. Filter input controls should create one + * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that + * wish to displayed filtered data should create one `FilterHandle` and use + * the {@link FilterHandle#filteredKeys} property and listen for change + * events. + * + * If two (or more) `FilterHandle` instances in the same webpage share the + * same group name, they will contribute to a single "filter set". Each + * `FilterHandle` starts out with a `null` value, which means they take + * nothing away from the set of data that should be shown. To make a + * `FilterHandle` actually remove data from the filter set, set its value to + * an array of keys which should be displayed. Crosstalk will aggregate the + * various key arrays by finding their intersection; only keys that are + * present in all non-null filter handles are considered part of the filter + * set. + * + * @param {string} [group] - The name of the Crosstalk group, or if none, + * null or undefined (or any other falsy value). This can be changed later + * via the {@link FilterHandle#setGroup} method. + * @param {Object} [extraInfo] - An object whose properties will be copied to + * the event object whenever an event is emitted. + */ + +var FilterHandle = exports.FilterHandle = function () { + function FilterHandle(group, extraInfo) { + _classCallCheck(this, FilterHandle); + + this._eventRelay = new _events2.default(); + this._emitter = new util.SubscriptionTracker(this._eventRelay); + + // Name of the group we're currently tracking, if any. Can change over time. + this._group = null; + // The filterSet that we're tracking, if any. Can change over time. + this._filterSet = null; + // The Var we're currently tracking, if any. Can change over time. + this._filterVar = null; + // The event handler subscription we currently have on var.on("change"). + this._varOnChangeSub = null; + + this._extraInfo = util.extend({ sender: this }, extraInfo); + + this._id = "filter" + nextId(); + + this.setGroup(group); + } + + /** + * Changes the Crosstalk group membership of this FilterHandle. If `set()` was + * previously called on this handle, switching groups will clear those keys + * from the old group's filter set. These keys will not be applied to the new + * group's filter set either. In other words, `setGroup()` effectively calls + * `clear()` before switching groups. + * + * @param {string} group - The name of the Crosstalk group, or null (or + * undefined) to clear the group. + */ + + + _createClass(FilterHandle, [{ + key: "setGroup", + value: function setGroup(group) { + var _this = this; + + // If group is unchanged, do nothing + if (this._group === group) return; + // Treat null, undefined, and other falsy values the same + if (!this._group && !group) return; + + if (this._filterVar) { + this._filterVar.off("change", this._varOnChangeSub); + this.clear(); + this._varOnChangeSub = null; + this._filterVar = null; + this._filterSet = null; + } + + this._group = group; + + if (group) { + group = (0, _group2.default)(group); + this._filterSet = getFilterSet(group); + this._filterVar = (0, _group2.default)(group).var("filter"); + var sub = this._filterVar.on("change", function (e) { + _this._eventRelay.trigger("change", e, _this); + }); + this._varOnChangeSub = sub; + } + } + + /** + * Combine the given `extraInfo` (if any) with the handle's default + * `_extraInfo` (if any). + * @private + */ + + }, { + key: "_mergeExtraInfo", + value: function _mergeExtraInfo(extraInfo) { + return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null); + } + + /** + * Close the handle. This clears this handle's contribution to the filter set, + * and unsubscribes all event listeners. + */ + + }, { + key: "close", + value: function close() { + this._emitter.removeAllListeners(); + this.clear(); + this.setGroup(null); + } + + /** + * Clear this handle's contribution to the filter set. + * + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `FilterHandle` constructor). + * + * @fires FilterHandle#change + */ + + }, { + key: "clear", + value: function clear(extraInfo) { + if (!this._filterSet) return; + this._filterSet.clear(this._id); + this._onChange(extraInfo); + } + + /** + * Set this handle's contribution to the filter set. This array should consist + * of the keys of the rows that _should_ be displayed; any keys that are not + * present in the array will be considered _filtered out_. Note that multiple + * `FilterHandle` instances in the group may each contribute an array of keys, + * and only those keys that appear in _all_ of the arrays make it through the + * filter. + * + * @param {string[]} keys - Empty array, or array of keys. To clear the + * filter, don't pass an empty array; instead, use the + * {@link FilterHandle#clear} method. + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `FilterHandle` constructor). + * + * @fires FilterHandle#change + */ + + }, { + key: "set", + value: function set(keys, extraInfo) { + if (!this._filterSet) return; + this._filterSet.update(this._id, keys); + this._onChange(extraInfo); + } + + /** + * @return {string[]|null} - Either: 1) an array of keys that made it through + * all of the `FilterHandle` instances, or, 2) `null`, which means no filter + * is being applied (all data should be displayed). + */ + + }, { + key: "on", + + + /** + * Subscribe to events on this `FilterHandle`. + * + * @param {string} eventType - Indicates the type of events to listen to. + * Currently, only `"change"` is supported. + * @param {FilterHandle~listener} listener - The callback function that + * will be invoked when the event occurs. + * @return {string} - A token to pass to {@link FilterHandle#off} to cancel + * this subscription. + */ + value: function on(eventType, listener) { + return this._emitter.on(eventType, listener); + } + + /** + * Cancel event subscriptions created by {@link FilterHandle#on}. + * + * @param {string} eventType - The type of event to unsubscribe. + * @param {string|FilterHandle~listener} listener - Either the callback + * function previously passed into {@link FilterHandle#on}, or the + * string that was returned from {@link FilterHandle#on}. + */ + + }, { + key: "off", + value: function off(eventType, listener) { + return this._emitter.off(eventType, listener); + } + }, { + key: "_onChange", + value: function _onChange(extraInfo) { + if (!this._filterSet) return; + this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo)); + } + + /** + * @callback FilterHandle~listener + * @param {Object} event - An object containing details of the event. For + * `"change"` events, this includes the properties `value` (the new + * value of the filter set, or `null` if no filter set is active), + * `oldValue` (the previous value of the filter set), and `sender` (the + * `FilterHandle` instance that made the change). + */ + + }, { + key: "filteredKeys", + get: function get() { + return this._filterSet ? this._filterSet.value : null; + } + }]); + + return FilterHandle; +}(); + +/** + * @event FilterHandle#change + * @type {object} + * @property {object} value - The new value of the filter set, or `null` + * if no filter set is active. + * @property {object} oldValue - The previous value of the filter set. + * @property {FilterHandle} sender - The `FilterHandle` instance that + * changed the value. + */ + +},{"./events":1,"./filterset":3,"./group":4,"./util":11}],3:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _util = require("./util"); + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function naturalComparator(a, b) { + if (a === b) { + return 0; + } else if (a < b) { + return -1; + } else if (a > b) { + return 1; + } +} + +/** + * @private + */ + +var FilterSet = function () { + function FilterSet() { + _classCallCheck(this, FilterSet); + + this.reset(); + } + + _createClass(FilterSet, [{ + key: "reset", + value: function reset() { + // Key: handle ID, Value: array of selected keys, or null + this._handles = {}; + // Key: key string, Value: count of handles that include it + this._keys = {}; + this._value = null; + this._activeHandles = 0; + } + }, { + key: "update", + value: function update(handleId, keys) { + if (keys !== null) { + keys = keys.slice(0); // clone before sorting + keys.sort(naturalComparator); + } + + var _diffSortedLists = (0, _util.diffSortedLists)(this._handles[handleId], keys), + added = _diffSortedLists.added, + removed = _diffSortedLists.removed; + + this._handles[handleId] = keys; + + for (var i = 0; i < added.length; i++) { + this._keys[added[i]] = (this._keys[added[i]] || 0) + 1; + } + for (var _i = 0; _i < removed.length; _i++) { + this._keys[removed[_i]]--; + } + + this._updateValue(keys); + } + + /** + * @param {string[]} keys Sorted array of strings that indicate + * a superset of possible keys. + * @private + */ + + }, { + key: "_updateValue", + value: function _updateValue() { + var keys = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : this._allKeys; + + var handleCount = Object.keys(this._handles).length; + if (handleCount === 0) { + this._value = null; + } else { + this._value = []; + for (var i = 0; i < keys.length; i++) { + var count = this._keys[keys[i]]; + if (count === handleCount) { + this._value.push(keys[i]); + } + } + } + } + }, { + key: "clear", + value: function clear(handleId) { + if (typeof this._handles[handleId] === "undefined") { + return; + } + + var keys = this._handles[handleId]; + if (!keys) { + keys = []; + } + + for (var i = 0; i < keys.length; i++) { + this._keys[keys[i]]--; + } + delete this._handles[handleId]; + + this._updateValue(); + } + }, { + key: "value", + get: function get() { + return this._value; + } + }, { + key: "_allKeys", + get: function get() { + var allKeys = Object.keys(this._keys); + allKeys.sort(naturalComparator); + return allKeys; + } + }]); + + return FilterSet; +}(); + +exports.default = FilterSet; + +},{"./util":11}],4:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.default = group; + +var _var2 = require("./var"); + +var _var3 = _interopRequireDefault(_var2); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +// Use a global so that multiple copies of crosstalk.js can be loaded and still +// have groups behave as singletons across all copies. +global.__crosstalk_groups = global.__crosstalk_groups || {}; +var groups = global.__crosstalk_groups; + +function group(groupName) { + if (groupName && typeof groupName === "string") { + if (!groups.hasOwnProperty(groupName)) { + groups[groupName] = new Group(groupName); + } + return groups[groupName]; + } else if ((typeof groupName === "undefined" ? "undefined" : _typeof(groupName)) === "object" && groupName._vars && groupName.var) { + // Appears to already be a group object + return groupName; + } else if (Array.isArray(groupName) && groupName.length == 1 && typeof groupName[0] === "string") { + return group(groupName[0]); + } else { + throw new Error("Invalid groupName argument"); + } +} + +var Group = function () { + function Group(name) { + _classCallCheck(this, Group); + + this.name = name; + this._vars = {}; + } + + _createClass(Group, [{ + key: "var", + value: function _var(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + if (!this._vars.hasOwnProperty(name)) this._vars[name] = new _var3.default(this, name); + return this._vars[name]; + } + }, { + key: "has", + value: function has(name) { + if (!name || typeof name !== "string") { + throw new Error("Invalid var name"); + } + + return this._vars.hasOwnProperty(name); + } + }]); + + return Group; +}(); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./var":12}],5:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _selection = require("./selection"); + +var _filter = require("./filter"); + +var _input = require("./input"); + +require("./input_selectize"); + +require("./input_checkboxgroup"); + +require("./input_slider"); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +var defaultGroup = (0, _group2.default)("default"); + +function var_(name) { + return defaultGroup.var(name); +} + +function has(name) { + return defaultGroup.has(name); +} + +if (global.Shiny) { + global.Shiny.addCustomMessageHandler("update-client-value", function (message) { + if (typeof message.group === "string") { + (0, _group2.default)(message.group).var(message.name).set(message.value); + } else { + var_(message.name).set(message.value); + } + }); +} + +var crosstalk = { + group: _group2.default, + var: var_, + has: has, + SelectionHandle: _selection.SelectionHandle, + FilterHandle: _filter.FilterHandle, + bind: _input.bind +}; + +/** + * @namespace crosstalk + */ +exports.default = crosstalk; + +global.crosstalk = crosstalk; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.register = register; +exports.bind = bind; +var $ = global.jQuery; + +var bindings = {}; + +function register(reg) { + bindings[reg.className] = reg; + if (global.document && global.document.readyState !== "complete") { + $(function () { + bind(); + }); + } else if (global.document) { + setTimeout(bind, 100); + } +} + +function bind() { + Object.keys(bindings).forEach(function (className) { + var binding = bindings[className]; + $("." + binding.className).not(".crosstalk-input-bound").each(function (i, el) { + bindInstance(binding, el); + }); + }); +} + +// Escape jQuery identifier +function $escape(val) { + return val.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g, "\\$1"); +} + +function bindEl(el) { + var $el = $(el); + Object.keys(bindings).forEach(function (className) { + if ($el.hasClass(className) && !$el.hasClass("crosstalk-input-bound")) { + var binding = bindings[className]; + bindInstance(binding, el); + } + }); +} + +function bindInstance(binding, el) { + var jsonEl = $(el).find("script[type='application/json'][data-for='" + $escape(el.id) + "']"); + var data = JSON.parse(jsonEl[0].innerText); + + var instance = binding.factory(el, data); + $(el).data("crosstalk-instance", instance); + $(el).addClass("crosstalk-input-bound"); +} + +if (global.Shiny) { + var inputBinding = new global.Shiny.InputBinding(); + var _$ = global.jQuery; + _$.extend(inputBinding, { + find: function find(scope) { + return _$(scope).find(".crosstalk-input"); + }, + initialize: function initialize(el) { + if (!_$(el).hasClass("crosstalk-input-bound")) { + bindEl(el); + } + }, + getId: function getId(el) { + return el.id; + }, + getValue: function getValue(el) {}, + setValue: function setValue(el, value) {}, + receiveMessage: function receiveMessage(el, data) {}, + subscribe: function subscribe(el, callback) { + _$(el).data("crosstalk-instance").resume(); + }, + unsubscribe: function unsubscribe(el) { + _$(el).data("crosstalk-instance").suspend(); + } + }); + global.Shiny.inputBindings.register(inputBinding, "crosstalk.inputBinding"); +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{}],7:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-checkboxgroup", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + var $el = $(el); + $el.on("change", "input[type='checkbox']", function () { + var checked = $el.find("input[type='checkbox']:checked"); + if (checked.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + checked.each(function () { + data.map[this.value].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],8:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; + +input.register({ + className: "crosstalk-input-select", + + factory: function factory(el, data) { + /* + * items: {value: [...], label: [...]} + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + + var first = [{ value: "", label: "(All)" }]; + var items = util.dataframeToD3(data.items); + var opts = { + options: first.concat(items), + valueField: "value", + labelField: "label", + searchField: "label" + }; + + var select = $(el).find("select")[0]; + + var selectize = $(select).selectize(opts)[0].selectize; + + var ctHandle = new _filter.FilterHandle(data.group); + + var lastKnownKeys = void 0; + selectize.on("change", function () { + if (selectize.items.length === 0) { + lastKnownKeys = null; + ctHandle.clear(); + } else { + var keys = {}; + selectize.items.forEach(function (group) { + data.map[group].forEach(function (key) { + keys[key] = true; + }); + }); + var keyArray = Object.keys(keys); + keyArray.sort(); + lastKnownKeys = keyArray; + ctHandle.set(keyArray); + } + }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6,"./util":11}],9:[function(require,module,exports){ +(function (global){ +"use strict"; + +var _slicedToArray = function () { function sliceIterator(arr, i) { var _arr = []; var _n = true; var _d = false; var _e = undefined; try { for (var _i = arr[Symbol.iterator](), _s; !(_n = (_s = _i.next()).done); _n = true) { _arr.push(_s.value); if (i && _arr.length === i) break; } } catch (err) { _d = true; _e = err; } finally { try { if (!_n && _i["return"]) _i["return"](); } finally { if (_d) throw _e; } } return _arr; } return function (arr, i) { if (Array.isArray(arr)) { return arr; } else if (Symbol.iterator in Object(arr)) { return sliceIterator(arr, i); } else { throw new TypeError("Invalid attempt to destructure non-iterable instance"); } }; }(); + +var _input = require("./input"); + +var input = _interopRequireWildcard(_input); + +var _filter = require("./filter"); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +var $ = global.jQuery; +var strftime = global.strftime; + +input.register({ + className: "crosstalk-input-slider", + + factory: function factory(el, data) { + /* + * map: {"groupA": ["keyA", "keyB", ...], ...} + * group: "ct-groupname" + */ + var ctHandle = new _filter.FilterHandle(data.group); + + var opts = {}; + var $el = $(el).find("input"); + var dataType = $el.data("data-type"); + var timeFormat = $el.data("time-format"); + var round = $el.data("round"); + var timeFormatter = void 0; + + // Set up formatting functions + if (dataType === "date") { + timeFormatter = strftime.utc(); + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "datetime") { + var timezone = $el.data("timezone"); + if (timezone) timeFormatter = strftime.timezone(timezone);else timeFormatter = strftime; + + opts.prettify = function (num) { + return timeFormatter(timeFormat, new Date(num)); + }; + } else if (dataType === "number") { + if (typeof round !== "undefined") opts.prettify = function (num) { + var factor = Math.pow(10, round); + return Math.round(num * factor) / factor; + }; + } + + $el.ionRangeSlider(opts); + + function getValue() { + var result = $el.data("ionRangeSlider").result; + + // Function for converting numeric value from slider to appropriate type. + var convert = void 0; + var dataType = $el.data("data-type"); + if (dataType === "date") { + convert = function convert(val) { + return formatDateUTC(new Date(+val)); + }; + } else if (dataType === "datetime") { + convert = function convert(val) { + // Convert ms to s + return +val / 1000; + }; + } else { + convert = function convert(val) { + return +val; + }; + } + + if ($el.data("ionRangeSlider").options.type === "double") { + return [convert(result.from), convert(result.to)]; + } else { + return convert(result.from); + } + } + + var lastKnownKeys = null; + + $el.on("change.crosstalkSliderInput", function (event) { + if (!$el.data("updating") && !$el.data("animating")) { + var _getValue = getValue(), + _getValue2 = _slicedToArray(_getValue, 2), + from = _getValue2[0], + to = _getValue2[1]; + + var keys = []; + for (var i = 0; i < data.values.length; i++) { + var val = data.values[i]; + if (val >= from && val <= to) { + keys.push(data.keys[i]); + } + } + keys.sort(); + ctHandle.set(keys); + lastKnownKeys = keys; + } + }); + + // let $el = $(el); + // $el.on("change", "input[type="checkbox"]", function() { + // let checked = $el.find("input[type="checkbox"]:checked"); + // if (checked.length === 0) { + // ctHandle.clear(); + // } else { + // let keys = {}; + // checked.each(function() { + // data.map[this.value].forEach(function(key) { + // keys[key] = true; + // }); + // }); + // let keyArray = Object.keys(keys); + // keyArray.sort(); + // ctHandle.set(keyArray); + // } + // }); + + return { + suspend: function suspend() { + ctHandle.clear(); + }, + resume: function resume() { + if (lastKnownKeys) ctHandle.set(lastKnownKeys); + } + }; + } +}); + +// Convert a number to a string with leading zeros +function padZeros(n, digits) { + var str = n.toString(); + while (str.length < digits) { + str = "0" + str; + }return str; +} + +// Given a Date object, return a string in yyyy-mm-dd format, using the +// UTC date. This may be a day off from the date in the local time zone. +function formatDateUTC(date) { + if (date instanceof Date) { + return date.getUTCFullYear() + "-" + padZeros(date.getUTCMonth() + 1, 2) + "-" + padZeros(date.getUTCDate(), 2); + } else { + return null; + } +} + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./filter":2,"./input":6}],10:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); +exports.SelectionHandle = undefined; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +var _group = require("./group"); + +var _group2 = _interopRequireDefault(_group); + +var _util = require("./util"); + +var util = _interopRequireWildcard(_util); + +function _interopRequireWildcard(obj) { if (obj && obj.__esModule) { return obj; } else { var newObj = {}; if (obj != null) { for (var key in obj) { if (Object.prototype.hasOwnProperty.call(obj, key)) newObj[key] = obj[key]; } } newObj.default = obj; return newObj; } } + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +/** + * Use this class to read and write (and listen for changes to) the selection + * for a Crosstalk group. This is intended to be used for linked brushing. + * + * If two (or more) `SelectionHandle` instances in the same webpage share the + * same group name, they will share the same state. Setting the selection using + * one `SelectionHandle` instance will result in the `value` property instantly + * changing across the others, and `"change"` event listeners on all instances + * (including the one that initiated the sending) will fire. + * + * @param {string} [group] - The name of the Crosstalk group, or if none, + * null or undefined (or any other falsy value). This can be changed later + * via the [SelectionHandle#setGroup](#setGroup) method. + * @param {Object} [extraInfo] - An object whose properties will be copied to + * the event object whenever an event is emitted. + */ +var SelectionHandle = exports.SelectionHandle = function () { + function SelectionHandle() { + var group = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : null; + var extraInfo = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : null; + + _classCallCheck(this, SelectionHandle); + + this._eventRelay = new _events2.default(); + this._emitter = new util.SubscriptionTracker(this._eventRelay); + + // Name of the group we're currently tracking, if any. Can change over time. + this._group = null; + // The Var we're currently tracking, if any. Can change over time. + this._var = null; + // The event handler subscription we currently have on var.on("change"). + this._varOnChangeSub = null; + + this._extraInfo = util.extend({ sender: this }, extraInfo); + + this.setGroup(group); + } + + /** + * Changes the Crosstalk group membership of this SelectionHandle. The group + * being switched away from (if any) will not have its selection value + * modified as a result of calling `setGroup`, even if this handle was the + * most recent handle to set the selection of the group. + * + * The group being switched to (if any) will also not have its selection value + * modified as a result of calling `setGroup`. If you want to set the + * selection value of the new group, call `set` explicitly. + * + * @param {string} group - The name of the Crosstalk group, or null (or + * undefined) to clear the group. + */ + + + _createClass(SelectionHandle, [{ + key: "setGroup", + value: function setGroup(group) { + var _this = this; + + // If group is unchanged, do nothing + if (this._group === group) return; + // Treat null, undefined, and other falsy values the same + if (!this._group && !group) return; + + if (this._var) { + this._var.off("change", this._varOnChangeSub); + this._var = null; + this._varOnChangeSub = null; + } + + this._group = group; + + if (group) { + this._var = (0, _group2.default)(group).var("selection"); + var sub = this._var.on("change", function (e) { + _this._eventRelay.trigger("change", e, _this); + }); + this._varOnChangeSub = sub; + } + } + + /** + * Retrieves the current selection for the group represented by this + * `SelectionHandle`. + * + * - If no selection is active, then this value will be falsy. + * - If a selection is active, but no data points are selected, then this + * value will be an empty array. + * - If a selection is active, and data points are selected, then the keys + * of the selected data points will be present in the array. + */ + + }, { + key: "_mergeExtraInfo", + + + /** + * Combines the given `extraInfo` (if any) with the handle's default + * `_extraInfo` (if any). + * @private + */ + value: function _mergeExtraInfo(extraInfo) { + // Important incidental effect: shallow clone is returned + return util.extend({}, this._extraInfo ? this._extraInfo : null, extraInfo ? extraInfo : null); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see + * {@link SelectionHandle#value}). + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any options that were + * passed into the `SelectionHandle` constructor). + */ + + }, { + key: "set", + value: function set(selectedKeys, extraInfo) { + if (this._var) this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo)); + } + + /** + * Overwrites the current selection for the group, and raises the `"change"` + * event among all of the group's '`SelectionHandle` instances (including + * this one). + * + * @fires SelectionHandle#change + * @param {Object} [extraInfo] - Extra properties to be included on the event + * object that's passed to listeners (in addition to any that were passed + * into the `SelectionHandle` constructor). + */ + + }, { + key: "clear", + value: function clear(extraInfo) { + if (this._var) this.set(void 0, this._mergeExtraInfo(extraInfo)); + } + + /** + * Subscribes to events on this `SelectionHandle`. + * + * @param {string} eventType - Indicates the type of events to listen to. + * Currently, only `"change"` is supported. + * @param {SelectionHandle~listener} listener - The callback function that + * will be invoked when the event occurs. + * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel + * this subscription. + */ + + }, { + key: "on", + value: function on(eventType, listener) { + return this._emitter.on(eventType, listener); + } + + /** + * Cancels event subscriptions created by {@link SelectionHandle#on}. + * + * @param {string} eventType - The type of event to unsubscribe. + * @param {string|SelectionHandle~listener} listener - Either the callback + * function previously passed into {@link SelectionHandle#on}, or the + * string that was returned from {@link SelectionHandle#on}. + */ + + }, { + key: "off", + value: function off(eventType, listener) { + return this._emitter.off(eventType, listener); + } + + /** + * Shuts down the `SelectionHandle` object. + * + * Removes all event listeners that were added through this handle. + */ + + }, { + key: "close", + value: function close() { + this._emitter.removeAllListeners(); + this.setGroup(null); + } + }, { + key: "value", + get: function get() { + return this._var ? this._var.get() : null; + } + }]); + + return SelectionHandle; +}(); + +/** + * @callback SelectionHandle~listener + * @param {Object} event - An object containing details of the event. For + * `"change"` events, this includes the properties `value` (the new + * value of the selection, or `undefined` if no selection is active), + * `oldValue` (the previous value of the selection), and `sender` (the + * `SelectionHandle` instance that made the change). + */ + +/** + * @event SelectionHandle#change + * @type {object} + * @property {object} value - The new value of the selection, or `undefined` + * if no selection is active. + * @property {object} oldValue - The previous value of the selection. + * @property {SelectionHandle} sender - The `SelectionHandle` instance that + * changed the value. + */ + +},{"./events":1,"./group":4,"./util":11}],11:[function(require,module,exports){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +exports.extend = extend; +exports.checkSorted = checkSorted; +exports.diffSortedLists = diffSortedLists; +exports.dataframeToD3 = dataframeToD3; + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +function extend(target) { + for (var _len = arguments.length, sources = Array(_len > 1 ? _len - 1 : 0), _key = 1; _key < _len; _key++) { + sources[_key - 1] = arguments[_key]; + } + + for (var i = 0; i < sources.length; i++) { + var src = sources[i]; + if (typeof src === "undefined" || src === null) continue; + + for (var key in src) { + if (src.hasOwnProperty(key)) { + target[key] = src[key]; + } + } + } + return target; +} + +function checkSorted(list) { + for (var i = 1; i < list.length; i++) { + if (list[i] <= list[i - 1]) { + throw new Error("List is not sorted or contains duplicate"); + } + } +} + +function diffSortedLists(a, b) { + var i_a = 0; + var i_b = 0; + + if (!a) a = []; + if (!b) b = []; + + var a_only = []; + var b_only = []; + + checkSorted(a); + checkSorted(b); + + while (i_a < a.length && i_b < b.length) { + if (a[i_a] === b[i_b]) { + i_a++; + i_b++; + } else if (a[i_a] < b[i_b]) { + a_only.push(a[i_a++]); + } else { + b_only.push(b[i_b++]); + } + } + + if (i_a < a.length) a_only = a_only.concat(a.slice(i_a)); + if (i_b < b.length) b_only = b_only.concat(b.slice(i_b)); + return { + removed: a_only, + added: b_only + }; +} + +// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... } +// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ] +function dataframeToD3(df) { + var names = []; + var length = void 0; + for (var name in df) { + if (df.hasOwnProperty(name)) names.push(name); + if (_typeof(df[name]) !== "object" || typeof df[name].length === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof length !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item = void 0; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; +} + +/** + * Keeps track of all event listener additions/removals and lets all active + * listeners be removed with a single operation. + * + * @private + */ + +var SubscriptionTracker = exports.SubscriptionTracker = function () { + function SubscriptionTracker(emitter) { + _classCallCheck(this, SubscriptionTracker); + + this._emitter = emitter; + this._subs = {}; + } + + _createClass(SubscriptionTracker, [{ + key: "on", + value: function on(eventType, listener) { + var sub = this._emitter.on(eventType, listener); + this._subs[sub] = eventType; + return sub; + } + }, { + key: "off", + value: function off(eventType, listener) { + var sub = this._emitter.off(eventType, listener); + if (sub) { + delete this._subs[sub]; + } + return sub; + } + }, { + key: "removeAllListeners", + value: function removeAllListeners() { + var _this = this; + + var current_subs = this._subs; + this._subs = {}; + Object.keys(current_subs).forEach(function (sub) { + _this._emitter.off(current_subs[sub], sub); + }); + } + }]); + + return SubscriptionTracker; +}(); + +},{}],12:[function(require,module,exports){ +(function (global){ +"use strict"; + +Object.defineProperty(exports, "__esModule", { + value: true +}); + +var _typeof = typeof Symbol === "function" && typeof Symbol.iterator === "symbol" ? function (obj) { return typeof obj; } : function (obj) { return obj && typeof Symbol === "function" && obj.constructor === Symbol && obj !== Symbol.prototype ? "symbol" : typeof obj; }; + +var _createClass = function () { function defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if ("value" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } } return function (Constructor, protoProps, staticProps) { if (protoProps) defineProperties(Constructor.prototype, protoProps); if (staticProps) defineProperties(Constructor, staticProps); return Constructor; }; }(); + +var _events = require("./events"); + +var _events2 = _interopRequireDefault(_events); + +function _interopRequireDefault(obj) { return obj && obj.__esModule ? obj : { default: obj }; } + +function _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError("Cannot call a class as a function"); } } + +var Var = function () { + function Var(group, name, /*optional*/value) { + _classCallCheck(this, Var); + + this._group = group; + this._name = name; + this._value = value; + this._events = new _events2.default(); + } + + _createClass(Var, [{ + key: "get", + value: function get() { + return this._value; + } + }, { + key: "set", + value: function set(value, /*optional*/event) { + if (this._value === value) { + // Do nothing; the value hasn't changed + return; + } + var oldValue = this._value; + this._value = value; + // Alert JavaScript listeners that the value has changed + var evt = {}; + if (event && (typeof event === "undefined" ? "undefined" : _typeof(event)) === "object") { + for (var k in event) { + if (event.hasOwnProperty(k)) evt[k] = event[k]; + } + } + evt.oldValue = oldValue; + evt.value = value; + this._events.trigger("change", evt, this); + + // TODO: Make this extensible, to let arbitrary back-ends know that + // something has changed + if (global.Shiny && global.Shiny.onInputChange) { + global.Shiny.onInputChange(".clientValue-" + (this._group.name !== null ? this._group.name + "-" : "") + this._name, typeof value === "undefined" ? null : value); + } + } + }, { + key: "on", + value: function on(eventType, listener) { + return this._events.on(eventType, listener); + } + }, { + key: "off", + value: function off(eventType, listener) { + return this._events.off(eventType, listener); + } + }]); + + return Var; +}(); + +exports.default = Var; + +}).call(this,typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) + +},{"./events":1}]},{},[5]) +//# sourceMappingURL=crosstalk.js.map diff --git a/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js.map b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js.map new file mode 100644 index 00000000..cff94f08 --- /dev/null +++ b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.js.map @@ -0,0 +1,37 @@ +{ + "version": 3, + "sources": [ + "node_modules/browser-pack/_prelude.js", + "javascript/src/events.js", + "javascript/src/filter.js", + "javascript/src/filterset.js", + "javascript/src/group.js", + "javascript/src/index.js", + "javascript/src/input.js", + "javascript/src/input_checkboxgroup.js", + "javascript/src/input_selectize.js", + "javascript/src/input_slider.js", + "javascript/src/selection.js", + "javascript/src/util.js", + "javascript/src/var.js" + ], + "names": [], + "mappings": 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+ "file": "generated.js", + "sourceRoot": "", + "sourcesContent": [ + "(function(){function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()", + "export default class Events {\n constructor() {\n this._types = {};\n this._seq = 0;\n }\n\n on(eventType, listener) {\n let subs = this._types[eventType];\n if (!subs) {\n subs = this._types[eventType] = {};\n }\n let sub = \"sub\" + (this._seq++);\n subs[sub] = listener;\n return sub;\n }\n\n // Returns false if no match, or string for sub name if matched\n off(eventType, listener) {\n let subs = this._types[eventType];\n if (typeof(listener) === \"function\") {\n for (let key in subs) {\n if (subs.hasOwnProperty(key)) {\n if (subs[key] === listener) {\n delete subs[key];\n return key;\n }\n }\n }\n return false;\n } else if (typeof(listener) === \"string\") {\n if (subs && subs[listener]) {\n delete subs[listener];\n return listener;\n }\n return false;\n } else {\n throw new Error(\"Unexpected type for listener\");\n }\n }\n\n trigger(eventType, arg, thisObj) {\n let subs = this._types[eventType];\n for (let key in subs) {\n if (subs.hasOwnProperty(key)) {\n subs[key].call(thisObj, arg);\n }\n }\n }\n}\n", + "import Events from \"./events\";\nimport FilterSet from \"./filterset\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nfunction getFilterSet(group) {\n let fsVar = group.var(\"filterset\");\n let result = fsVar.get();\n if (!result) {\n result = new FilterSet();\n fsVar.set(result);\n }\n return result;\n}\n\nlet id = 1;\nfunction nextId() {\n return id++;\n}\n\n/**\n * Use this class to contribute to, and listen for changes to, the filter set\n * for the given group of widgets. Filter input controls should create one\n * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that\n * wish to displayed filtered data should create one `FilterHandle` and use\n * the {@link FilterHandle#filteredKeys} property and listen for change\n * events.\n *\n * If two (or more) `FilterHandle` instances in the same webpage share the\n * same group name, they will contribute to a single \"filter set\". Each\n * `FilterHandle` starts out with a `null` value, which means they take\n * nothing away from the set of data that should be shown. To make a\n * `FilterHandle` actually remove data from the filter set, set its value to\n * an array of keys which should be displayed. Crosstalk will aggregate the\n * various key arrays by finding their intersection; only keys that are\n * present in all non-null filter handles are considered part of the filter\n * set.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the {@link FilterHandle#setGroup} method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class FilterHandle {\n constructor(group, extraInfo) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The filterSet that we're tracking, if any. Can change over time.\n this._filterSet = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._filterVar = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this._id = \"filter\" + nextId();\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this FilterHandle. If `set()` was\n * previously called on this handle, switching groups will clear those keys\n * from the old group's filter set. These keys will not be applied to the new\n * group's filter set either. In other words, `setGroup()` effectively calls\n * `clear()` before switching groups.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._filterVar) {\n this._filterVar.off(\"change\", this._varOnChangeSub);\n this.clear();\n this._varOnChangeSub = null;\n this._filterVar = null;\n this._filterSet = null;\n }\n\n this._group = group;\n\n if (group) {\n group = grp(group);\n this._filterSet = getFilterSet(group);\n this._filterVar = grp(group).var(\"filter\");\n let sub = this._filterVar.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n", + "import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n", + "import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n", + "import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n", + "let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n", + "import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n", + "import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n", + "export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n", + "import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n" + ] +}
\ No newline at end of file diff --git a/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.min.js b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.min.js new file mode 100644 index 00000000..b7ec0ac9 --- /dev/null +++ b/docs/coverage/lib/crosstalk-1.2.1/js/crosstalk.min.js @@ -0,0 +1,2 @@ +!function o(u,a,l){function s(n,e){if(!a[n]){if(!u[n]){var t="function"==typeof require&&require;if(!e&&t)return t(n,!0);if(f)return f(n,!0);var r=new Error("Cannot find module '"+n+"'");throw r.code="MODULE_NOT_FOUND",r}var i=a[n]={exports:{}};u[n][0].call(i.exports,function(e){var t=u[n][1][e];return s(t||e)},i,i.exports,o,u,a,l)}return a[n].exports}for(var f="function"==typeof require&&require,e=0;e<l.length;e++)s(l[e]);return s}({1:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(){function r(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}();var i=function(){function e(){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,e),this._types={},this._seq=0}return r(e,[{key:"on",value:function(e,t){var n=this._types[e];n||(n=this._types[e]={});var r="sub"+this._seq++;return n[r]=t,r}},{key:"off",value:function(e,t){var n=this._types[e];if("function"==typeof t){for(var r in n)if(n.hasOwnProperty(r)&&n[r]===t)return delete n[r],r;return!1}if("string"==typeof t)return!(!n||!n[t])&&(delete n[t],t);throw new Error("Unexpected type for listener")}},{key:"trigger",value:function(e,t,n){var r=this._types[e];for(var i in r)r.hasOwnProperty(i)&&r[i].call(n,t)}}]),e}();n.default=i},{}],2:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0}),n.FilterHandle=void 0;var r=function(){function r(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),i=l(e("./events")),o=l(e("./filterset")),u=l(e("./group")),a=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(e("./util"));function l(e){return e&&e.__esModule?e:{default:e}}var s=1;n.FilterHandle=function(){function n(e,t){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,n),this._eventRelay=new i.default,this._emitter=new a.SubscriptionTracker(this._eventRelay),this._group=null,this._filterSet=null,this._filterVar=null,this._varOnChangeSub=null,this._extraInfo=a.extend({sender:this},t),this._id="filter"+s++,this.setGroup(e)}return r(n,[{key:"setGroup",value:function(e){var t,n,r=this;if(this._group!==e&&((this._group||e)&&(this._filterVar&&(this._filterVar.off("change",this._varOnChangeSub),this.clear(),this._varOnChangeSub=null,this._filterVar=null,this._filterSet=null),this._group=e))){e=(0,u.default)(e),this._filterSet=(t=e.var("filterset"),(n=t.get())||(n=new o.default,t.set(n)),n),this._filterVar=(0,u.default)(e).var("filter");var i=this._filterVar.on("change",function(e){r._eventRelay.trigger("change",e,r)});this._varOnChangeSub=i}}},{key:"_mergeExtraInfo",value:function(e){return a.extend({},this._extraInfo?this._extraInfo:null,e||null)}},{key:"close",value:function(){this._emitter.removeAllListeners(),this.clear(),this.setGroup(null)}},{key:"clear",value:function(e){this._filterSet&&(this._filterSet.clear(this._id),this._onChange(e))}},{key:"set",value:function(e,t){this._filterSet&&(this._filterSet.update(this._id,e),this._onChange(t))}},{key:"on",value:function(e,t){return this._emitter.on(e,t)}},{key:"off",value:function(e,t){return this._emitter.off(e,t)}},{key:"_onChange",value:function(e){this._filterSet&&this._filterVar.set(this._filterSet.value,this._mergeExtraInfo(e))}},{key:"filteredKeys",get:function(){return this._filterSet?this._filterSet.value:null}}]),n}()},{"./events":1,"./filterset":3,"./group":4,"./util":11}],3:[function(e,t,n){"use strict";Object.defineProperty(n,"__esModule",{value:!0});var r=function(){function r(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),a=e("./util");function l(e,t){return e===t?0:e<t?-1:t<e?1:void 0}var i=function(){function e(){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,e),this.reset()}return r(e,[{key:"reset",value:function(){this._handles={},this._keys={},this._value=null,this._activeHandles=0}},{key:"update",value:function(e,t){null!==t&&(t=t.slice(0)).sort(l);var n=(0,a.diffSortedLists)(this._handles[e],t),r=n.added,i=n.removed;this._handles[e]=t;for(var o=0;o<r.length;o++)this._keys[r[o]]=(this._keys[r[o]]||0)+1;for(var u=0;u<i.length;u++)this._keys[i[u]]--;this._updateValue(t)}},{key:"_updateValue",value:function(){var e=0<arguments.length&&void 0!==arguments[0]?arguments[0]:this._allKeys,t=Object.keys(this._handles).length;if(0===t)this._value=null;else{this._value=[];for(var n=0;n<e.length;n++){this._keys[e[n]]===t&&this._value.push(e[n])}}}},{key:"clear",value:function(e){if(void 0!==this._handles[e]){var t=this._handles[e];t||(t=[]);for(var n=0;n<t.length;n++)this._keys[t[n]]--;delete this._handles[e],this._updateValue()}}},{key:"value",get:function(){return this._value}},{key:"_allKeys",get:function(){var e=Object.keys(this._keys);return e.sort(l),e}}]),e}();n.default=i},{"./util":11}],4:[function(l,e,s){(function(e){"use strict";Object.defineProperty(s,"__esModule",{value:!0});var n=function(){function r(e,t){for(var n=0;n<t.length;n++){var r=t[n];r.enumerable=r.enumerable||!1,r.configurable=!0,"value"in r&&(r.writable=!0),Object.defineProperty(e,r.key,r)}}return function(e,t,n){return t&&r(e.prototype,t),n&&r(e,n),e}}(),r="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(e){return typeof e}:function(e){return e&&"function"==typeof Symbol&&e.constructor===Symbol&&e!==Symbol.prototype?"symbol":typeof e};s.default=function e(t){{if(t&&"string"==typeof t)return u.hasOwnProperty(t)||(u[t]=new a(t)),u[t];if("object"===(void 0===t?"undefined":r(t))&&t._vars&&t.var)return t;if(Array.isArray(t)&&1==t.length&&"string"==typeof t[0])return e(t[0]);throw new Error("Invalid groupName argument")}};var t,i=l("./var"),o=(t=i)&&t.__esModule?t:{default:t};e.__crosstalk_groups=e.__crosstalk_groups||{};var u=e.__crosstalk_groups;var a=function(){function t(e){!function(e,t){if(!(e instanceof t))throw new TypeError("Cannot call a class as a function")}(this,t),this.name=e,this._vars={}}return n(t,[{key:"var",value:function(e){if(!e||"string"!=typeof e)throw new Error("Invalid var name");return this._vars.hasOwnProperty(e)||(this._vars[e]=new o.default(this,e)),this._vars[e]}},{key:"has",value:function(e){if(!e||"string"!=typeof e)throw new Error("Invalid var name");return this._vars.hasOwnProperty(e)}}]),t}()}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./var":12}],5:[function(f,e,c){(function(e){"use strict";Object.defineProperty(c,"__esModule",{value:!0});var t,n=f("./group"),r=(t=n)&&t.__esModule?t:{default:t},i=f("./selection"),o=f("./filter"),u=f("./input");f("./input_selectize"),f("./input_checkboxgroup"),f("./input_slider");var a=(0,r.default)("default");function l(e){return a.var(e)}e.Shiny&&e.Shiny.addCustomMessageHandler("update-client-value",function(e){"string"==typeof e.group?(0,r.default)(e.group).var(e.name).set(e.value):l(e.name).set(e.value)});var s={group:r.default,var:l,has:function(e){return a.has(e)},SelectionHandle:i.SelectionHandle,FilterHandle:o.FilterHandle,bind:u.bind};c.default=s,e.crosstalk=s}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./group":4,"./input":6,"./input_checkboxgroup":7,"./input_selectize":8,"./input_slider":9,"./selection":10}],6:[function(e,t,a){(function(t){"use strict";Object.defineProperty(a,"__esModule",{value:!0}),a.register=function(e){r[e.className]=e,t.document&&"complete"!==t.document.readyState?o(function(){n()}):t.document&&setTimeout(n,100)},a.bind=n;var o=t.jQuery,r={};function n(){Object.keys(r).forEach(function(e){var n=r[e];o("."+n.className).not(".crosstalk-input-bound").each(function(e,t){i(n,t)})})}function i(e,t){var n=o(t).find("script[type='application/json'][data-for='"+t.id.replace(/([!"#$%&'()*+,./:;<=>?@[\\\]^`{|}~])/g,"\\$1")+"']"),r=JSON.parse(n[0].innerText),i=e.factory(t,r);o(t).data("crosstalk-instance",i),o(t).addClass("crosstalk-input-bound")}if(t.Shiny){var e=new t.Shiny.InputBinding,u=t.jQuery;u.extend(e,{find:function(e){return u(e).find(".crosstalk-input")},initialize:function(e){var t,n;u(e).hasClass("crosstalk-input-bound")||(n=o(t=e),Object.keys(r).forEach(function(e){n.hasClass(e)&&!n.hasClass("crosstalk-input-bound")&&i(r[e],t)}))},getId:function(e){return e.id},getValue:function(e){},setValue:function(e,t){},receiveMessage:function(e,t){},subscribe:function(e,t){u(e).data("crosstalk-instance").resume()},unsubscribe:function(e){u(e).data("crosstalk-instance").suspend()}}),t.Shiny.inputBindings.register(e,"crosstalk.inputBinding")}}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{}],7:[function(r,e,t){(function(e){"use strict";var t=function(e){{if(e&&e.__esModule)return e;var t={};if(null!=e)for(var n in e)Object.prototype.hasOwnProperty.call(e,n)&&(t[n]=e[n]);return t.default=e,t}}(r("./input")),n=r("./filter");var a=e.jQuery;t.register({className:"crosstalk-input-checkboxgroup",factory:function(e,r){var i=new n.FilterHandle(r.group),o=void 0,u=a(e);return u.on("change","input[type='checkbox']",function(){var e=u.find("input[type='checkbox']:checked");if(0===e.length)o=null,i.clear();else{var t={};e.each(function(){r.map[this.value].forEach(function(e){t[e]=!0})});var n=Object.keys(t);n.sort(),o=n,i.set(n)}}),{suspend:function(){i.clear()},resume:function(){o&&i.set(o)}}}})}).call(this,"undefined"!=typeof global?global:"undefined"!=typeof self?self:"undefined"!=typeof window?window:{})},{"./filter":2,"./input":6}],8:[function(r,e,t){(function(e){"use strict";var t=n(r("./input")),l=n(r("./util")),s=r("./filter");function 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e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require==\"function\"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error(\"Cannot find module '\"+o+\"'\");throw f.code=\"MODULE_NOT_FOUND\",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require==\"function\"&&require;for(var o=0;o<r.length;o++)s(r[o]);return s}return e})()","export default class Events {\n constructor() {\n this._types = {};\n this._seq = 0;\n }\n\n on(eventType, listener) {\n let subs = this._types[eventType];\n if (!subs) {\n subs = this._types[eventType] = {};\n }\n let sub = \"sub\" + (this._seq++);\n subs[sub] = listener;\n return sub;\n }\n\n // Returns false if no match, or string for sub name if matched\n off(eventType, listener) {\n let subs = this._types[eventType];\n if (typeof(listener) === \"function\") {\n for (let key in subs) {\n if (subs.hasOwnProperty(key)) {\n if (subs[key] === listener) {\n delete subs[key];\n return key;\n }\n }\n }\n return false;\n } else if (typeof(listener) === \"string\") {\n if (subs && subs[listener]) {\n delete subs[listener];\n return listener;\n }\n return false;\n } else {\n throw new Error(\"Unexpected type for listener\");\n }\n }\n\n trigger(eventType, arg, thisObj) {\n let subs = this._types[eventType];\n for (let key in subs) {\n if (subs.hasOwnProperty(key)) {\n subs[key].call(thisObj, arg);\n }\n }\n }\n}\n","import Events from \"./events\";\nimport FilterSet from \"./filterset\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\nfunction getFilterSet(group) {\n let fsVar = group.var(\"filterset\");\n let result = fsVar.get();\n if (!result) {\n result = new FilterSet();\n fsVar.set(result);\n }\n return result;\n}\n\nlet id = 1;\nfunction nextId() {\n return id++;\n}\n\n/**\n * Use this class to contribute to, and listen for changes to, the filter set\n * for the given group of widgets. Filter input controls should create one\n * `FilterHandle` and only call {@link FilterHandle#set}. Output widgets that\n * wish to displayed filtered data should create one `FilterHandle` and use\n * the {@link FilterHandle#filteredKeys} property and listen for change\n * events.\n *\n * If two (or more) `FilterHandle` instances in the same webpage share the\n * same group name, they will contribute to a single \"filter set\". Each\n * `FilterHandle` starts out with a `null` value, which means they take\n * nothing away from the set of data that should be shown. To make a\n * `FilterHandle` actually remove data from the filter set, set its value to\n * an array of keys which should be displayed. Crosstalk will aggregate the\n * various key arrays by finding their intersection; only keys that are\n * present in all non-null filter handles are considered part of the filter\n * set.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the {@link FilterHandle#setGroup} method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class FilterHandle {\n constructor(group, extraInfo) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The filterSet that we're tracking, if any. Can change over time.\n this._filterSet = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._filterVar = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this._id = \"filter\" + nextId();\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this FilterHandle. If `set()` was\n * previously called on this handle, switching groups will clear those keys\n * from the old group's filter set. These keys will not be applied to the new\n * group's filter set either. In other words, `setGroup()` effectively calls\n * `clear()` before switching groups.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._filterVar) {\n this._filterVar.off(\"change\", this._varOnChangeSub);\n this.clear();\n this._varOnChangeSub = null;\n this._filterVar = null;\n this._filterSet = null;\n }\n\n this._group = group;\n\n if (group) {\n group = grp(group);\n this._filterSet = getFilterSet(group);\n this._filterVar = grp(group).var(\"filter\");\n let sub = this._filterVar.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Combine the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Close the handle. This clears this handle's contribution to the filter set,\n * and unsubscribes all event listeners.\n */\n close() {\n this._emitter.removeAllListeners();\n this.clear();\n this.setGroup(null);\n }\n\n /**\n * Clear this handle's contribution to the filter set.\n *\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n clear(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.clear(this._id);\n this._onChange(extraInfo);\n }\n\n /**\n * Set this handle's contribution to the filter set. This array should consist\n * of the keys of the rows that _should_ be displayed; any keys that are not\n * present in the array will be considered _filtered out_. Note that multiple\n * `FilterHandle` instances in the group may each contribute an array of keys,\n * and only those keys that appear in _all_ of the arrays make it through the\n * filter.\n *\n * @param {string[]} keys - Empty array, or array of keys. To clear the\n * filter, don't pass an empty array; instead, use the\n * {@link FilterHandle#clear} method.\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `FilterHandle` constructor).\n * \n * @fires FilterHandle#change\n */\n set(keys, extraInfo) {\n if (!this._filterSet)\n return;\n this._filterSet.update(this._id, keys);\n this._onChange(extraInfo);\n }\n\n /**\n * @return {string[]|null} - Either: 1) an array of keys that made it through\n * all of the `FilterHandle` instances, or, 2) `null`, which means no filter\n * is being applied (all data should be displayed).\n */\n get filteredKeys() {\n return this._filterSet ? this._filterSet.value : null;\n }\n\n /**\n * Subscribe to events on this `FilterHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {FilterHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link FilterHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancel event subscriptions created by {@link FilterHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|FilterHandle~listener} listener - Either the callback\n * function previously passed into {@link FilterHandle#on}, or the\n * string that was returned from {@link FilterHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n _onChange(extraInfo) {\n if (!this._filterSet)\n return;\n this._filterVar.set(this._filterSet.value, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * @callback FilterHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the filter set, or `null` if no filter set is active),\n * `oldValue` (the previous value of the filter set), and `sender` (the\n * `FilterHandle` instance that made the change).\n */\n\n}\n\n/**\n * @event FilterHandle#change\n * @type {object}\n * @property {object} value - The new value of the filter set, or `null`\n * if no filter set is active.\n * @property {object} oldValue - The previous value of the filter set.\n * @property {FilterHandle} sender - The `FilterHandle` instance that\n * changed the value.\n */\n","import { diffSortedLists } from \"./util\";\n\nfunction naturalComparator(a, b) {\n if (a === b) {\n return 0;\n } else if (a < b) {\n return -1;\n } else if (a > b) {\n return 1;\n }\n}\n\n/**\n * @private\n */\nexport default class FilterSet {\n constructor() {\n this.reset();\n }\n\n reset() {\n // Key: handle ID, Value: array of selected keys, or null\n this._handles = {};\n // Key: key string, Value: count of handles that include it\n this._keys = {};\n this._value = null;\n this._activeHandles = 0;\n }\n\n get value() {\n return this._value;\n }\n\n update(handleId, keys) {\n if (keys !== null) {\n keys = keys.slice(0); // clone before sorting\n keys.sort(naturalComparator);\n }\n\n let {added, removed} = diffSortedLists(this._handles[handleId], keys);\n this._handles[handleId] = keys;\n\n for (let i = 0; i < added.length; i++) {\n this._keys[added[i]] = (this._keys[added[i]] || 0) + 1;\n }\n for (let i = 0; i < removed.length; i++) {\n this._keys[removed[i]]--;\n }\n\n this._updateValue(keys);\n }\n\n /**\n * @param {string[]} keys Sorted array of strings that indicate\n * a superset of possible keys.\n * @private\n */\n _updateValue(keys = this._allKeys) {\n let handleCount = Object.keys(this._handles).length;\n if (handleCount === 0) {\n this._value = null;\n } else {\n this._value = [];\n for (let i = 0; i < keys.length; i++) {\n let count = this._keys[keys[i]];\n if (count === handleCount) {\n this._value.push(keys[i]);\n }\n }\n }\n }\n\n clear(handleId) {\n if (typeof(this._handles[handleId]) === \"undefined\") {\n return;\n }\n\n let keys = this._handles[handleId];\n if (!keys) {\n keys = [];\n }\n\n for (let i = 0; i < keys.length; i++) {\n this._keys[keys[i]]--;\n }\n delete this._handles[handleId];\n\n this._updateValue();\n }\n\n get _allKeys() {\n let allKeys = Object.keys(this._keys);\n allKeys.sort(naturalComparator);\n return allKeys;\n }\n}\n","import Var from \"./var\";\n\n// Use a global so that multiple copies of crosstalk.js can be loaded and still\n// have groups behave as singletons across all copies.\nglobal.__crosstalk_groups = global.__crosstalk_groups || {};\nlet groups = global.__crosstalk_groups;\n\nexport default function group(groupName) {\n if (groupName && typeof(groupName) === \"string\") {\n if (!groups.hasOwnProperty(groupName)) {\n groups[groupName] = new Group(groupName);\n }\n return groups[groupName];\n } else if (typeof(groupName) === \"object\" && groupName._vars && groupName.var) {\n // Appears to already be a group object\n return groupName;\n } else if (Array.isArray(groupName) &&\n groupName.length == 1 &&\n typeof(groupName[0]) === \"string\") {\n return group(groupName[0]);\n } else {\n throw new Error(\"Invalid groupName argument\");\n }\n}\n\nclass Group {\n constructor(name) {\n this.name = name;\n this._vars = {};\n }\n\n var(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n if (!this._vars.hasOwnProperty(name))\n this._vars[name] = new Var(this, name);\n return this._vars[name];\n }\n\n has(name) {\n if (!name || typeof(name) !== \"string\") {\n throw new Error(\"Invalid var name\");\n }\n\n return this._vars.hasOwnProperty(name);\n }\n}\n","import group from \"./group\";\nimport { SelectionHandle } from \"./selection\";\nimport { FilterHandle } from \"./filter\";\nimport { bind } from \"./input\";\nimport \"./input_selectize\";\nimport \"./input_checkboxgroup\";\nimport \"./input_slider\";\n\nconst defaultGroup = group(\"default\");\n\nfunction var_(name) {\n return defaultGroup.var(name);\n}\n\nfunction has(name) {\n return defaultGroup.has(name);\n}\n\nif (global.Shiny) {\n global.Shiny.addCustomMessageHandler(\"update-client-value\", function(message) {\n if (typeof(message.group) === \"string\") {\n group(message.group).var(message.name).set(message.value);\n } else {\n var_(message.name).set(message.value);\n }\n });\n}\n\nconst crosstalk = {\n group: group,\n var: var_,\n has: has,\n SelectionHandle: SelectionHandle,\n FilterHandle: FilterHandle,\n bind: bind\n};\n\n/**\n * @namespace crosstalk\n */\nexport default crosstalk;\nglobal.crosstalk = crosstalk;\n","let $ = global.jQuery;\n\nlet bindings = {};\n\nexport function register(reg) {\n bindings[reg.className] = reg;\n if (global.document && global.document.readyState !== \"complete\") {\n $(() => {\n bind();\n });\n } else if (global.document) {\n setTimeout(bind, 100);\n }\n}\n\nexport function bind() {\n Object.keys(bindings).forEach(function(className) {\n let binding = bindings[className];\n $(\".\" + binding.className).not(\".crosstalk-input-bound\").each(function(i, el) {\n bindInstance(binding, el);\n });\n });\n}\n\n// Escape jQuery identifier\nfunction $escape(val) {\n return val.replace(/([!\"#$%&'()*+,./:;<=>?@[\\\\\\]^`{|}~])/g, \"\\\\$1\");\n}\n\nfunction bindEl(el) {\n let $el = $(el);\n Object.keys(bindings).forEach(function(className) {\n if ($el.hasClass(className) && !$el.hasClass(\"crosstalk-input-bound\")) {\n let binding = bindings[className];\n bindInstance(binding, el);\n }\n });\n}\n\nfunction bindInstance(binding, el) {\n let jsonEl = $(el).find(\"script[type='application/json'][data-for='\" + $escape(el.id) + \"']\");\n let data = JSON.parse(jsonEl[0].innerText);\n\n let instance = binding.factory(el, data);\n $(el).data(\"crosstalk-instance\", instance);\n $(el).addClass(\"crosstalk-input-bound\");\n}\n\nif (global.Shiny) {\n let inputBinding = new global.Shiny.InputBinding();\n let $ = global.jQuery;\n $.extend(inputBinding, {\n find: function(scope) {\n return $(scope).find(\".crosstalk-input\");\n },\n initialize: function(el) {\n if (!$(el).hasClass(\"crosstalk-input-bound\")) {\n bindEl(el);\n }\n },\n getId: function(el) {\n return el.id;\n },\n getValue: function(el) {\n\n },\n setValue: function(el, value) {\n\n },\n receiveMessage: function(el, data) {\n\n },\n subscribe: function(el, callback) {\n $(el).data(\"crosstalk-instance\").resume();\n },\n unsubscribe: function(el) {\n $(el).data(\"crosstalk-instance\").suspend();\n }\n });\n global.Shiny.inputBindings.register(inputBinding, \"crosstalk.inputBinding\");\n}\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-checkboxgroup\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n let $el = $(el);\n $el.on(\"change\", \"input[type='checkbox']\", function() {\n let checked = $el.find(\"input[type='checkbox']:checked\");\n if (checked.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n checked.each(function() {\n data.map[this.value].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport * as util from \"./util\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\n\ninput.register({\n className: \"crosstalk-input-select\",\n\n factory: function(el, data) {\n /*\n * items: {value: [...], label: [...]}\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n\n let first = [{value: \"\", label: \"(All)\"}];\n let items = util.dataframeToD3(data.items);\n let opts = {\n options: first.concat(items),\n valueField: \"value\",\n labelField: \"label\",\n searchField: \"label\"\n };\n\n let select = $(el).find(\"select\")[0];\n\n let selectize = $(select).selectize(opts)[0].selectize;\n\n let ctHandle = new FilterHandle(data.group);\n\n let lastKnownKeys;\n selectize.on(\"change\", function() {\n if (selectize.items.length === 0) {\n lastKnownKeys = null;\n ctHandle.clear();\n } else {\n let keys = {};\n selectize.items.forEach(function(group) {\n data.map[group].forEach(function(key) {\n keys[key] = true;\n });\n });\n let keyArray = Object.keys(keys);\n keyArray.sort();\n lastKnownKeys = keyArray;\n ctHandle.set(keyArray);\n }\n });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n","import * as input from \"./input\";\nimport { FilterHandle } from \"./filter\";\n\nlet $ = global.jQuery;\nlet strftime = global.strftime;\n\ninput.register({\n className: \"crosstalk-input-slider\",\n\n factory: function(el, data) {\n /*\n * map: {\"groupA\": [\"keyA\", \"keyB\", ...], ...}\n * group: \"ct-groupname\"\n */\n let ctHandle = new FilterHandle(data.group);\n\n let opts = {};\n let $el = $(el).find(\"input\");\n let dataType = $el.data(\"data-type\");\n let timeFormat = $el.data(\"time-format\");\n let round = $el.data(\"round\");\n let timeFormatter;\n\n // Set up formatting functions\n if (dataType === \"date\") {\n timeFormatter = strftime.utc();\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n\n } else if (dataType === \"datetime\") {\n let timezone = $el.data(\"timezone\");\n if (timezone)\n timeFormatter = strftime.timezone(timezone);\n else\n timeFormatter = strftime;\n\n opts.prettify = function(num) {\n return timeFormatter(timeFormat, new Date(num));\n };\n } else if (dataType === \"number\") {\n if (typeof round !== \"undefined\")\n opts.prettify = function(num) {\n let factor = Math.pow(10, round);\n return Math.round(num * factor) / factor;\n };\n }\n\n $el.ionRangeSlider(opts);\n\n function getValue() {\n let result = $el.data(\"ionRangeSlider\").result;\n\n // Function for converting numeric value from slider to appropriate type.\n let convert;\n let dataType = $el.data(\"data-type\");\n if (dataType === \"date\") {\n convert = function(val) {\n return formatDateUTC(new Date(+val));\n };\n } else if (dataType === \"datetime\") {\n convert = function(val) {\n // Convert ms to s\n return +val / 1000;\n };\n } else {\n convert = function(val) { return +val; };\n }\n\n if ($el.data(\"ionRangeSlider\").options.type === \"double\") {\n return [convert(result.from), convert(result.to)];\n } else {\n return convert(result.from);\n }\n }\n\n let lastKnownKeys = null;\n\n $el.on(\"change.crosstalkSliderInput\", function(event) {\n if (!$el.data(\"updating\") && !$el.data(\"animating\")) {\n let [from, to] = getValue();\n let keys = [];\n for (let i = 0; i < data.values.length; i++) {\n let val = data.values[i];\n if (val >= from && val <= to) {\n keys.push(data.keys[i]);\n }\n }\n keys.sort();\n ctHandle.set(keys);\n lastKnownKeys = keys;\n }\n });\n\n\n // let $el = $(el);\n // $el.on(\"change\", \"input[type=\"checkbox\"]\", function() {\n // let checked = $el.find(\"input[type=\"checkbox\"]:checked\");\n // if (checked.length === 0) {\n // ctHandle.clear();\n // } else {\n // let keys = {};\n // checked.each(function() {\n // data.map[this.value].forEach(function(key) {\n // keys[key] = true;\n // });\n // });\n // let keyArray = Object.keys(keys);\n // keyArray.sort();\n // ctHandle.set(keyArray);\n // }\n // });\n\n return {\n suspend: function() {\n ctHandle.clear();\n },\n resume: function() {\n if (lastKnownKeys)\n ctHandle.set(lastKnownKeys);\n }\n };\n }\n});\n\n\n// Convert a number to a string with leading zeros\nfunction padZeros(n, digits) {\n let str = n.toString();\n while (str.length < digits)\n str = \"0\" + str;\n return str;\n}\n\n// Given a Date object, return a string in yyyy-mm-dd format, using the\n// UTC date. This may be a day off from the date in the local time zone.\nfunction formatDateUTC(date) {\n if (date instanceof Date) {\n return date.getUTCFullYear() + \"-\" +\n padZeros(date.getUTCMonth()+1, 2) + \"-\" +\n padZeros(date.getUTCDate(), 2);\n\n } else {\n return null;\n }\n}\n","import Events from \"./events\";\nimport grp from \"./group\";\nimport * as util from \"./util\";\n\n/**\n * Use this class to read and write (and listen for changes to) the selection\n * for a Crosstalk group. This is intended to be used for linked brushing.\n *\n * If two (or more) `SelectionHandle` instances in the same webpage share the\n * same group name, they will share the same state. Setting the selection using\n * one `SelectionHandle` instance will result in the `value` property instantly\n * changing across the others, and `\"change\"` event listeners on all instances\n * (including the one that initiated the sending) will fire.\n *\n * @param {string} [group] - The name of the Crosstalk group, or if none,\n * null or undefined (or any other falsy value). This can be changed later\n * via the [SelectionHandle#setGroup](#setGroup) method.\n * @param {Object} [extraInfo] - An object whose properties will be copied to\n * the event object whenever an event is emitted.\n */\nexport class SelectionHandle {\n\n constructor(group = null, extraInfo = null) {\n this._eventRelay = new Events();\n this._emitter = new util.SubscriptionTracker(this._eventRelay);\n\n // Name of the group we're currently tracking, if any. Can change over time.\n this._group = null;\n // The Var we're currently tracking, if any. Can change over time.\n this._var = null;\n // The event handler subscription we currently have on var.on(\"change\").\n this._varOnChangeSub = null;\n\n this._extraInfo = util.extend({ sender: this }, extraInfo);\n\n this.setGroup(group);\n }\n\n /**\n * Changes the Crosstalk group membership of this SelectionHandle. The group\n * being switched away from (if any) will not have its selection value\n * modified as a result of calling `setGroup`, even if this handle was the\n * most recent handle to set the selection of the group.\n *\n * The group being switched to (if any) will also not have its selection value\n * modified as a result of calling `setGroup`. If you want to set the\n * selection value of the new group, call `set` explicitly.\n *\n * @param {string} group - The name of the Crosstalk group, or null (or\n * undefined) to clear the group.\n */\n setGroup(group) {\n // If group is unchanged, do nothing\n if (this._group === group)\n return;\n // Treat null, undefined, and other falsy values the same\n if (!this._group && !group)\n return;\n\n if (this._var) {\n this._var.off(\"change\", this._varOnChangeSub);\n this._var = null;\n this._varOnChangeSub = null;\n }\n\n this._group = group;\n\n if (group) {\n this._var = grp(group).var(\"selection\");\n let sub = this._var.on(\"change\", (e) => {\n this._eventRelay.trigger(\"change\", e, this);\n });\n this._varOnChangeSub = sub;\n }\n }\n\n /**\n * Retrieves the current selection for the group represented by this\n * `SelectionHandle`.\n *\n * - If no selection is active, then this value will be falsy.\n * - If a selection is active, but no data points are selected, then this\n * value will be an empty array.\n * - If a selection is active, and data points are selected, then the keys\n * of the selected data points will be present in the array.\n */\n get value() {\n return this._var ? this._var.get() : null;\n }\n\n /**\n * Combines the given `extraInfo` (if any) with the handle's default\n * `_extraInfo` (if any).\n * @private\n */\n _mergeExtraInfo(extraInfo) {\n // Important incidental effect: shallow clone is returned\n return util.extend({},\n this._extraInfo ? this._extraInfo : null,\n extraInfo ? extraInfo : null);\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {string[]} selectedKeys - Falsy, empty array, or array of keys (see\n * {@link SelectionHandle#value}).\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any options that were\n * passed into the `SelectionHandle` constructor).\n */\n set(selectedKeys, extraInfo) {\n if (this._var)\n this._var.set(selectedKeys, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Overwrites the current selection for the group, and raises the `\"change\"`\n * event among all of the group's '`SelectionHandle` instances (including\n * this one).\n *\n * @fires SelectionHandle#change\n * @param {Object} [extraInfo] - Extra properties to be included on the event\n * object that's passed to listeners (in addition to any that were passed\n * into the `SelectionHandle` constructor).\n */\n clear(extraInfo) {\n if (this._var)\n this.set(void 0, this._mergeExtraInfo(extraInfo));\n }\n\n /**\n * Subscribes to events on this `SelectionHandle`.\n *\n * @param {string} eventType - Indicates the type of events to listen to.\n * Currently, only `\"change\"` is supported.\n * @param {SelectionHandle~listener} listener - The callback function that\n * will be invoked when the event occurs.\n * @return {string} - A token to pass to {@link SelectionHandle#off} to cancel\n * this subscription.\n */\n on(eventType, listener) {\n return this._emitter.on(eventType, listener);\n }\n\n /**\n * Cancels event subscriptions created by {@link SelectionHandle#on}.\n *\n * @param {string} eventType - The type of event to unsubscribe.\n * @param {string|SelectionHandle~listener} listener - Either the callback\n * function previously passed into {@link SelectionHandle#on}, or the\n * string that was returned from {@link SelectionHandle#on}.\n */\n off(eventType, listener) {\n return this._emitter.off(eventType, listener);\n }\n\n /**\n * Shuts down the `SelectionHandle` object.\n *\n * Removes all event listeners that were added through this handle.\n */\n close() {\n this._emitter.removeAllListeners();\n this.setGroup(null);\n }\n}\n\n/**\n * @callback SelectionHandle~listener\n * @param {Object} event - An object containing details of the event. For\n * `\"change\"` events, this includes the properties `value` (the new\n * value of the selection, or `undefined` if no selection is active),\n * `oldValue` (the previous value of the selection), and `sender` (the\n * `SelectionHandle` instance that made the change).\n */\n\n/**\n * @event SelectionHandle#change\n * @type {object}\n * @property {object} value - The new value of the selection, or `undefined`\n * if no selection is active.\n * @property {object} oldValue - The previous value of the selection.\n * @property {SelectionHandle} sender - The `SelectionHandle` instance that\n * changed the value.\n */\n","export function extend(target, ...sources) {\n for (let i = 0; i < sources.length; i++) {\n let src = sources[i];\n if (typeof(src) === \"undefined\" || src === null)\n continue;\n\n for (let key in src) {\n if (src.hasOwnProperty(key)) {\n target[key] = src[key];\n }\n }\n }\n return target;\n}\n\nexport function checkSorted(list) {\n for (let i = 1; i < list.length; i++) {\n if (list[i] <= list[i-1]) {\n throw new Error(\"List is not sorted or contains duplicate\");\n }\n }\n}\n\nexport function diffSortedLists(a, b) {\n let i_a = 0;\n let i_b = 0;\n\n if (!a) a = [];\n if (!b) b = [];\n\n let a_only = [];\n let b_only = [];\n\n checkSorted(a);\n checkSorted(b);\n\n while (i_a < a.length && i_b < b.length) {\n if (a[i_a] === b[i_b]) {\n i_a++;\n i_b++;\n } else if (a[i_a] < b[i_b]) {\n a_only.push(a[i_a++]);\n } else {\n b_only.push(b[i_b++]);\n }\n }\n\n if (i_a < a.length)\n a_only = a_only.concat(a.slice(i_a));\n if (i_b < b.length)\n b_only = b_only.concat(b.slice(i_b));\n return {\n removed: a_only,\n added: b_only\n };\n}\n\n// Convert from wide: { colA: [1,2,3], colB: [4,5,6], ... }\n// to long: [ {colA: 1, colB: 4}, {colA: 2, colB: 5}, ... ]\nexport function dataframeToD3(df) {\n let names = [];\n let length;\n for (let name in df) {\n if (df.hasOwnProperty(name))\n names.push(name);\n if (typeof(df[name]) !== \"object\" || typeof(df[name].length) === \"undefined\") {\n throw new Error(\"All fields must be arrays\");\n } else if (typeof(length) !== \"undefined\" && length !== df[name].length) {\n throw new Error(\"All fields must be arrays of the same length\");\n }\n length = df[name].length;\n }\n let results = [];\n let item;\n for (let row = 0; row < length; row++) {\n item = {};\n for (let col = 0; col < names.length; col++) {\n item[names[col]] = df[names[col]][row];\n }\n results.push(item);\n }\n return results;\n}\n\n/**\n * Keeps track of all event listener additions/removals and lets all active\n * listeners be removed with a single operation.\n *\n * @private\n */\nexport class SubscriptionTracker {\n constructor(emitter) {\n this._emitter = emitter;\n this._subs = {};\n }\n\n on(eventType, listener) {\n let sub = this._emitter.on(eventType, listener);\n this._subs[sub] = eventType;\n return sub;\n }\n\n off(eventType, listener) {\n let sub = this._emitter.off(eventType, listener);\n if (sub) {\n delete this._subs[sub];\n }\n return sub;\n }\n\n removeAllListeners() {\n let current_subs = this._subs;\n this._subs = {};\n Object.keys(current_subs).forEach((sub) => {\n this._emitter.off(current_subs[sub], sub);\n });\n }\n}\n","import Events from \"./events\";\n\nexport default class Var {\n constructor(group, name, /*optional*/ value) {\n this._group = group;\n this._name = name;\n this._value = value;\n this._events = new Events();\n }\n\n get() {\n return this._value;\n }\n\n set(value, /*optional*/ event) {\n if (this._value === value) {\n // Do nothing; the value hasn't changed\n return;\n }\n let oldValue = this._value;\n this._value = value;\n // Alert JavaScript listeners that the value has changed\n let evt = {};\n if (event && typeof(event) === \"object\") {\n for (let k in event) {\n if (event.hasOwnProperty(k))\n evt[k] = event[k];\n }\n }\n evt.oldValue = oldValue;\n evt.value = value;\n this._events.trigger(\"change\", evt, this);\n\n // TODO: Make this extensible, to let arbitrary back-ends know that\n // something has changed\n if (global.Shiny && global.Shiny.onInputChange) {\n global.Shiny.onInputChange(\n \".clientValue-\" +\n (this._group.name !== null ? this._group.name + \"-\" : \"\") +\n this._name,\n typeof(value) === \"undefined\" ? null : value\n );\n }\n }\n\n on(eventType, listener) {\n return this._events.on(eventType, listener);\n }\n\n off(eventType, listener) {\n return this._events.off(eventType, listener);\n }\n}\n"]}
\ No newline at end of file diff --git a/docs/coverage/lib/crosstalk-1.2.1/scss/crosstalk.scss b/docs/coverage/lib/crosstalk-1.2.1/scss/crosstalk.scss new file mode 100644 index 00000000..35665616 --- /dev/null +++ b/docs/coverage/lib/crosstalk-1.2.1/scss/crosstalk.scss @@ -0,0 +1,75 @@ +/* Adjust margins outwards, so column contents line up with the edges of the + parent of container-fluid. */ +.container-fluid.crosstalk-bscols { + margin-left: -30px; + margin-right: -30px; + white-space: normal; +} + +/* But don't adjust the margins outwards if we're directly under the body, + i.e. we were the top-level of something at the console. */ +body > .container-fluid.crosstalk-bscols { + margin-left: auto; + margin-right: auto; +} + +.crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: inline-block; + padding-right: 12px; + vertical-align: top; +} + +@media only screen and (max-width:480px) { + .crosstalk-input-checkboxgroup .crosstalk-options-group .crosstalk-options-column { + display: block; + padding-right: inherit; + } +} + +/* Relevant BS3 styles to make filter_checkbox() look reasonable without Bootstrap */ +.crosstalk-input { + margin-bottom: 15px; /* a la .form-group */ + .control-label { + margin-bottom: 0; + vertical-align: middle; + } + input[type="checkbox"] { + margin: 4px 0 0; + margin-top: 1px; + line-height: normal; + } + .checkbox { + position: relative; + display: block; + margin-top: 10px; + margin-bottom: 10px; + } + .checkbox > label{ + padding-left: 20px; + margin-bottom: 0; + font-weight: 400; + cursor: pointer; + } + .checkbox input[type="checkbox"], + .checkbox-inline input[type="checkbox"] { + position: absolute; + margin-top: 2px; + margin-left: -20px; + } + .checkbox + .checkbox { + margin-top: -5px; + } + .checkbox-inline { + position: relative; + display: inline-block; + padding-left: 20px; + margin-bottom: 0; + font-weight: 400; + vertical-align: middle; + cursor: pointer; + } + .checkbox-inline + .checkbox-inline { + margin-top: 0; + margin-left: 10px; + } +} diff --git a/docs/coverage/lib/datatables-binding-0.33/datatables.js b/docs/coverage/lib/datatables-binding-0.33/datatables.js new file mode 100644 index 00000000..765b53cb --- /dev/null +++ b/docs/coverage/lib/datatables-binding-0.33/datatables.js @@ -0,0 +1,1539 @@ +(function() { + +// some helper functions: using a global object DTWidget so that it can be used +// in JS() code, e.g. datatable(options = list(foo = JS('code'))); unlike R's +// dynamic scoping, when 'code' is eval'ed, JavaScript does not know objects +// from the "parent frame", e.g. JS('DTWidget') will not work unless it was made +// a global object +var DTWidget = {}; + +// 123456666.7890 -> 123,456,666.7890 +var markInterval = function(d, digits, interval, mark, decMark, precision) { + x = precision ? d.toPrecision(digits) : d.toFixed(digits); + if (!/^-?[\d.]+$/.test(x)) return x; + var xv = x.split('.'); + if (xv.length > 2) return x; // should have at most one decimal point + xv[0] = xv[0].replace(new RegExp('\\B(?=(\\d{' + interval + '})+(?!\\d))', 'g'), mark); + return xv.join(decMark); +}; + +DTWidget.formatCurrency = function(data, currency, digits, interval, mark, decMark, before, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + var res = markInterval(d, digits, interval, mark, decMark); + res = before ? (/^-/.test(res) ? '-' + currency + res.replace(/^-/, '') : currency + res) : + res + currency; + return res; +}; + +DTWidget.formatString = function(data, prefix, suffix) { + var d = data; + if (d === null) return ''; + return prefix + d + suffix; +}; + +DTWidget.formatPercentage = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d * 100, digits, interval, mark, decMark) + '%'; +}; + +DTWidget.formatRound = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark); +}; + +DTWidget.formatSignif = function(data, digits, interval, mark, decMark, zeroPrint) { + var d = parseFloat(data); + if (isNaN(d)) return ''; + if (zeroPrint !== null && d === 0.0) return zeroPrint; + return markInterval(d, digits, interval, mark, decMark, true); +}; + +DTWidget.formatDate = function(data, method, params) { + var d = data; + if (d === null) return ''; + // (new Date('2015-10-28')).toDateString() may return 2015-10-27 because the + // actual time created could be like 'Tue Oct 27 2015 19:00:00 GMT-0500 (CDT)', + // i.e. the date-only string is treated as UTC time instead of local time + if ((method === 'toDateString' || method === 'toLocaleDateString') && /^\d{4,}\D\d{2}\D\d{2}$/.test(d)) { + d = d.split(/\D/); + d = new Date(d[0], d[1] - 1, d[2]); + } else { + d = new Date(d); + } + return d[method].apply(d, params); +}; + +window.DTWidget = DTWidget; + +// A helper function to update the properties of existing filters +var setFilterProps = function(td, props) { + // Update enabled/disabled state + var $input = $(td).find('input').first(); + var searchable = $input.data('searchable'); + $input.prop('disabled', !searchable || props.disabled); + + // Based on the filter type, set its new values + var type = td.getAttribute('data-type'); + if (['factor', 'logical'].includes(type)) { + // Reformat the new dropdown options for use with selectize + var new_vals = props.params.options.map(function(item) { + return { text: item, value: item }; + }); + + // Find the selectize object + var dropdown = $(td).find('.selectized').eq(0)[0].selectize; + + // Note the current values + var old_vals = dropdown.getValue(); + + // Remove the existing values + dropdown.clearOptions(); + + // Add the new options + dropdown.addOption(new_vals); + + // Preserve the existing values + dropdown.setValue(old_vals); + + } else if (['number', 'integer', 'date', 'time'].includes(type)) { + // Apply internal scaling to new limits. Updating scale not yet implemented. + var slider = $(td).find('.noUi-target').eq(0); + var scale = Math.pow(10, Math.max(0, +slider.data('scale') || 0)); + var new_vals = [props.params.min * scale, props.params.max * scale]; + + // Note what the new limits will be just for this filter + var new_lims = new_vals.slice(); + + // Determine the current values and limits + var old_vals = slider.val().map(Number); + var old_lims = slider.noUiSlider('options').range; + old_lims = [old_lims.min, old_lims.max]; + + // Preserve the current values if filters have been applied; otherwise, apply no filtering + if (old_vals[0] != old_lims[0]) { + new_vals[0] = Math.max(old_vals[0], new_vals[0]); + } + + if (old_vals[1] != old_lims[1]) { + new_vals[1] = Math.min(old_vals[1], new_vals[1]); + } + + // Update the endpoints of the slider + slider.noUiSlider({ + start: new_vals, + range: {'min': new_lims[0], 'max': new_lims[1]} + }, true); + } +}; + +var transposeArray2D = function(a) { + return a.length === 0 ? a : HTMLWidgets.transposeArray2D(a); +}; + +var crosstalkPluginsInstalled = false; + +function maybeInstallCrosstalkPlugins() { + if (crosstalkPluginsInstalled) + return; + crosstalkPluginsInstalled = true; + + $.fn.dataTable.ext.afnFiltering.push( + function(oSettings, aData, iDataIndex) { + var ctfilter = oSettings.nTable.ctfilter; + if (ctfilter && !ctfilter[iDataIndex]) + return false; + + var ctselect = oSettings.nTable.ctselect; + if (ctselect && !ctselect[iDataIndex]) + return false; + + return true; + } + ); +} + +HTMLWidgets.widget({ + name: "datatables", + type: "output", + renderOnNullValue: true, + initialize: function(el, width, height) { + // in order that the type=number inputs return a number + $.valHooks.number = { + get: function(el) { + var value = parseFloat(el.value); + return isNaN(value) ? "" : value; + } + }; + $(el).html(' '); + return { + data: null, + ctfilterHandle: new crosstalk.FilterHandle(), + ctfilterSubscription: null, + ctselectHandle: new crosstalk.SelectionHandle(), + ctselectSubscription: null + }; + }, + renderValue: function(el, data, instance) { + if (el.offsetWidth === 0 || el.offsetHeight === 0) { + instance.data = data; + return; + } + instance.data = null; + var $el = $(el); + $el.empty(); + + if (data === null) { + $el.append(' '); + // clear previous Shiny inputs (if any) + for (var i in instance.clearInputs) instance.clearInputs[i](); + instance.clearInputs = {}; + return; + } + + var crosstalkOptions = data.crosstalkOptions; + if (!crosstalkOptions) crosstalkOptions = { + 'key': null, 'group': null + }; + if (crosstalkOptions.group) { + maybeInstallCrosstalkPlugins(); + instance.ctfilterHandle.setGroup(crosstalkOptions.group); + instance.ctselectHandle.setGroup(crosstalkOptions.group); + } + + // if we are in the viewer then we always want to fillContainer and + // and autoHideNavigation (unless the user has explicitly set these) + if (window.HTMLWidgets.viewerMode) { + if (!data.hasOwnProperty("fillContainer")) + data.fillContainer = true; + if (!data.hasOwnProperty("autoHideNavigation")) + data.autoHideNavigation = true; + } + + // propagate fillContainer to instance (so we have it in resize) + instance.fillContainer = data.fillContainer; + + var cells = data.data; + + if (cells instanceof Array) cells = transposeArray2D(cells); + + $el.append(data.container); + var $table = $el.find('table'); + if (data.class) $table.addClass(data.class); + if (data.caption) $table.prepend(data.caption); + + if (!data.selection) data.selection = { + mode: 'none', selected: null, target: 'row', selectable: null + }; + if (HTMLWidgets.shinyMode && data.selection.mode !== 'none' && + data.selection.target === 'row+column') { + if ($table.children('tfoot').length === 0) { + $table.append($('<tfoot>')); + $table.find('thead tr').clone().appendTo($table.find('tfoot')); + } + } + + // column filters + var filterRow; + switch (data.filter) { + case 'top': + $table.children('thead').append(data.filterHTML); + filterRow = $table.find('thead tr:last td'); + break; + case 'bottom': + if ($table.children('tfoot').length === 0) { + $table.append($('<tfoot>')); + } + $table.children('tfoot').prepend(data.filterHTML); + filterRow = $table.find('tfoot tr:first td'); + break; + } + + var options = { searchDelay: 1000 }; + if (cells !== null) $.extend(options, { + data: cells + }); + + // options for fillContainer + var bootstrapActive = typeof($.fn.popover) != 'undefined'; + if (instance.fillContainer) { + + // force scrollX/scrollY and turn off autoWidth + options.scrollX = true; + options.scrollY = "100px"; // can be any value, we'll adjust below + + // if we aren't paginating then move around the info/filter controls + // to save space at the bottom and rephrase the info callback + if (data.options.paging === false) { + + // we know how to do this cleanly for bootstrap, not so much + // for other themes/layouts + if (bootstrapActive) { + options.dom = "<'row'<'col-sm-4'i><'col-sm-8'f>>" + + "<'row'<'col-sm-12'tr>>"; + } + + options.fnInfoCallback = function(oSettings, iStart, iEnd, + iMax, iTotal, sPre) { + return Number(iTotal).toLocaleString() + " records"; + }; + } + } + + // auto hide navigation if requested + // Note, this only works on client-side processing mode as on server-side, + // cells (data.data) is null; In addition, we require the pageLength option + // being provided explicitly to enable this. Despite we may be able to deduce + // the default value of pageLength, it may complicate things so we'd rather + // put this responsiblity to users and warn them on the R side. + if (data.autoHideNavigation === true && data.options.paging !== false) { + // strip all nav if length >= cells + if ((cells instanceof Array) && data.options.pageLength >= cells.length) + options.dom = bootstrapActive ? "<'row'<'col-sm-12'tr>>" : "t"; + // alternatively lean things out for flexdashboard mobile portrait + else if (bootstrapActive && window.FlexDashboard && window.FlexDashboard.isMobilePhone()) + options.dom = "<'row'<'col-sm-12'f>>" + + "<'row'<'col-sm-12'tr>>" + + "<'row'<'col-sm-12'p>>"; + } + + $.extend(true, options, data.options || {}); + + var searchCols = options.searchCols; + if (searchCols) { + searchCols = searchCols.map(function(x) { + return x === null ? '' : x.search; + }); + // FIXME: this means I don't respect the escapeRegex setting + delete options.searchCols; + } + + // server-side processing? + var server = options.serverSide === true; + + // use the dataSrc function to pre-process JSON data returned from R + var DT_rows_all = [], DT_rows_current = []; + if (server && HTMLWidgets.shinyMode && typeof options.ajax === 'object' && + /^session\/[\da-z]+\/dataobj/.test(options.ajax.url) && !options.ajax.dataSrc) { + options.ajax.dataSrc = function(json) { + DT_rows_all = $.makeArray(json.DT_rows_all); + DT_rows_current = $.makeArray(json.DT_rows_current); + var data = json.data; + if (!colReorderEnabled()) return data; + var table = $table.DataTable(), order = table.colReorder.order(), flag = true, i, j, row; + for (i = 0; i < order.length; ++i) if (order[i] !== i) flag = false; + if (flag) return data; + for (i = 0; i < data.length; ++i) { + row = data[i].slice(); + for (j = 0; j < order.length; ++j) data[i][j] = row[order[j]]; + } + return data; + }; + } + + var thiz = this; + if (instance.fillContainer) $table.on('init.dt', function(e) { + thiz.fillAvailableHeight(el, $(el).innerHeight()); + }); + // If the page contains serveral datatables and one of which enables colReorder, + // the table.colReorder.order() function will exist but throws error when called. + // So it seems like the only way to know if colReorder is enabled or not is to + // check the options. + var colReorderEnabled = function() { return "colReorder" in options; }; + var table = $table.DataTable(options); + $el.data('datatable', table); + + if ('rowGroup' in options) { + // Maintain RowGroup dataSrc when columns are reordered (#1109) + table.on('column-reorder', function(e, settings, details) { + var oldDataSrc = table.rowGroup().dataSrc(); + var newDataSrc = details.mapping[oldDataSrc]; + table.rowGroup().dataSrc(newDataSrc); + }); + } + + // Unregister previous Crosstalk event subscriptions, if they exist + if (instance.ctfilterSubscription) { + instance.ctfilterHandle.off("change", instance.ctfilterSubscription); + instance.ctfilterSubscription = null; + } + if (instance.ctselectSubscription) { + instance.ctselectHandle.off("change", instance.ctselectSubscription); + instance.ctselectSubscription = null; + } + + if (!crosstalkOptions.group) { + $table[0].ctfilter = null; + $table[0].ctselect = null; + } else { + var key = crosstalkOptions.key; + function keysToMatches(keys) { + if (!keys) { + return null; + } else { + var selectedKeys = {}; + for (var i = 0; i < keys.length; i++) { + selectedKeys[keys[i]] = true; + } + var matches = {}; + for (var j = 0; j < key.length; j++) { + if (selectedKeys[key[j]]) + matches[j] = true; + } + return matches; + } + } + + function applyCrosstalkFilter(e) { + $table[0].ctfilter = keysToMatches(e.value); + table.draw(); + } + instance.ctfilterSubscription = instance.ctfilterHandle.on("change", applyCrosstalkFilter); + applyCrosstalkFilter({value: instance.ctfilterHandle.filteredKeys}); + + function applyCrosstalkSelection(e) { + if (e.sender !== instance.ctselectHandle) { + table + .rows('.' + selClass, {search: 'applied'}) + .nodes() + .to$() + .removeClass(selClass); + if (selectedRows) + changeInput('rows_selected', selectedRows(), void 0, true); + } + + if (e.sender !== instance.ctselectHandle && e.value && e.value.length) { + var matches = keysToMatches(e.value); + + // persistent selection with plotly (& leaflet) + var ctOpts = crosstalk.var("plotlyCrosstalkOpts").get() || {}; + if (ctOpts.persistent === true) { + var matches = $.extend(matches, $table[0].ctselect); + } + + $table[0].ctselect = matches; + table.draw(); + } else { + if ($table[0].ctselect) { + $table[0].ctselect = null; + table.draw(); + } + } + } + instance.ctselectSubscription = instance.ctselectHandle.on("change", applyCrosstalkSelection); + // TODO: This next line doesn't seem to work when renderDataTable is used + applyCrosstalkSelection({value: instance.ctselectHandle.value}); + } + + var inArray = function(val, array) { + return $.inArray(val, $.makeArray(array)) > -1; + }; + + // search the i-th column + var searchColumn = function(i, value) { + var regex = false, ci = true; + if (options.search) { + regex = options.search.regex, + ci = options.search.caseInsensitive !== false; + } + // need to transpose the column index when colReorder is enabled + if (table.colReorder) i = table.colReorder.transpose(i); + return table.column(i).search(value, regex, !regex, ci); + }; + + if (data.filter !== 'none') { + if (!data.hasOwnProperty('filterSettings')) data.filterSettings = {}; + + filterRow.each(function(i, td) { + + var $td = $(td), type = $td.data('type'), filter; + var $input = $td.children('div').first().children('input'); + var disabled = $input.prop('disabled'); + var searchable = table.settings()[0].aoColumns[i].bSearchable; + $input.prop('disabled', !searchable || disabled); + $input.data('searchable', searchable); // for updating later + $input.on('input blur', function() { + $input.next('span').toggle(Boolean($input.val())); + }); + // Bootstrap sets pointer-events to none and we won't be able to click + // the clear button + $input.next('span').css('pointer-events', 'auto').hide().click(function() { + $(this).hide().prev('input').val('').trigger('input').focus(); + }); + var searchCol; // search string for this column + if (searchCols && searchCols[i]) { + searchCol = searchCols[i]; + $input.val(searchCol).trigger('input'); + } + var $x = $td.children('div').last(); + + // remove the overflow: hidden attribute of the scrollHead + // (otherwise the scrolling table body obscures the filters) + // The workaround and the discussion from + // https://github.com/rstudio/DT/issues/554#issuecomment-518007347 + // Otherwise the filter selection will not be anchored to the values + // when the columns number is many and scrollX is enabled. + var scrollHead = $(el).find('.dataTables_scrollHead,.dataTables_scrollFoot'); + var cssOverflowHead = scrollHead.css('overflow'); + var scrollBody = $(el).find('.dataTables_scrollBody'); + var cssOverflowBody = scrollBody.css('overflow'); + var scrollTable = $(el).find('.dataTables_scroll'); + var cssOverflowTable = scrollTable.css('overflow'); + if (cssOverflowHead === 'hidden') { + $x.on('show hide', function(e) { + if (e.type === 'show') { + scrollHead.css('overflow', 'visible'); + scrollBody.css('overflow', 'visible'); + scrollTable.css('overflow-x', 'scroll'); + } else { + scrollHead.css('overflow', cssOverflowHead); + scrollBody.css('overflow', cssOverflowBody); + scrollTable.css('overflow-x', cssOverflowTable); + } + }); + $x.css('z-index', 25); + } + + if (inArray(type, ['factor', 'logical'])) { + $input.on({ + click: function() { + $input.parent().hide(); $x.show().trigger('show'); filter[0].selectize.focus(); + }, + input: function() { + var v1 = JSON.stringify(filter[0].selectize.getValue()), v2 = $input.val(); + if (v1 === '[]') v1 = ''; + if (v1 !== v2) filter[0].selectize.setValue(v2 === '' ? [] : JSON.parse(v2)); + } + }); + var $input2 = $x.children('select'); + filter = $input2.selectize($.extend({ + options: $input2.data('options').map(function(v, i) { + return ({text: v, value: v}); + }), + plugins: ['remove_button'], + hideSelected: true, + onChange: function(value) { + if (value === null) value = []; // compatibility with jQuery 3.0 + $input.val(value.length ? JSON.stringify(value) : ''); + if (value.length) $input.trigger('input'); + $input.attr('title', $input.val()); + if (server) { + searchColumn(i, value.length ? JSON.stringify(value) : '').draw(); + return; + } + // turn off filter if nothing selected + $td.data('filter', value.length > 0); + table.draw(); // redraw table, and filters will be applied + } + }, data.filterSettings.select)); + filter[0].selectize.on('blur', function() { + $x.hide().trigger('hide'); $input.parent().show(); $input.trigger('blur'); + }); + filter.next('div').css('margin-bottom', 'auto'); + } else if (type === 'character') { + var fun = function() { + searchColumn(i, $input.val()).draw(); + }; + // throttle searching for server-side processing + var throttledFun = $.fn.dataTable.util.throttle(fun, options.searchDelay); + $input.on('input', function(e, immediate) { + // always bypass throttling when immediate = true (via the updateSearch method) + (immediate || !server) ? fun() : throttledFun(); + }); + } else if (inArray(type, ['number', 'integer', 'date', 'time'])) { + var $x0 = $x; + $x = $x0.children('div').first(); + $x0.css({ + 'background-color': '#fff', + 'border': '1px #ddd solid', + 'border-radius': '4px', + 'padding': data.vertical ? '35px 20px': '20px 20px 10px 20px' + }); + var $spans = $x0.children('span').css({ + 'margin-top': data.vertical ? '0' : '10px', + 'white-space': 'nowrap' + }); + var $span1 = $spans.first(), $span2 = $spans.last(); + var r1 = +$x.data('min'), r2 = +$x.data('max'); + // when the numbers are too small or have many decimal places, the + // slider may have numeric precision problems (#150) + var scale = Math.pow(10, Math.max(0, +$x.data('scale') || 0)); + r1 = Math.round(r1 * scale); r2 = Math.round(r2 * scale); + var scaleBack = function(x, scale) { + if (scale === 1) return x; + var d = Math.round(Math.log(scale) / Math.log(10)); + // to avoid problems like 3.423/100 -> 0.034230000000000003 + return (x / scale).toFixed(d); + }; + var slider_min = function() { + return filter.noUiSlider('options').range.min; + }; + var slider_max = function() { + return filter.noUiSlider('options').range.max; + }; + $input.on({ + focus: function() { + $x0.show().trigger('show'); + // first, make sure the slider div leaves at least 20px between + // the two (slider value) span's + $x0.width(Math.max(160, $span1.outerWidth() + $span2.outerWidth() + 20)); + // then, if the input is really wide or slider is vertical, + // make the slider the same width as the input + if ($x0.outerWidth() < $input.outerWidth() || data.vertical) { + $x0.outerWidth($input.outerWidth()); + } + // make sure the slider div does not reach beyond the right margin + if ($(window).width() < $x0.offset().left + $x0.width()) { + $x0.offset({ + 'left': $input.offset().left + $input.outerWidth() - $x0.outerWidth() + }); + } + }, + blur: function() { + $x0.hide().trigger('hide'); + }, + input: function() { + if ($input.val() === '') filter.val([slider_min(), slider_max()]); + }, + change: function() { + var v = $input.val().replace(/\s/g, ''); + if (v === '') return; + v = v.split('...'); + if (v.length !== 2) { + $input.parent().addClass('has-error'); + return; + } + if (v[0] === '') v[0] = slider_min(); + if (v[1] === '') v[1] = slider_max(); + $input.parent().removeClass('has-error'); + // treat date as UTC time at midnight + var strTime = function(x) { + var s = type === 'date' ? 'T00:00:00Z' : ''; + var t = new Date(x + s).getTime(); + // add 10 minutes to date since it does not hurt the date, and + // it helps avoid the tricky floating point arithmetic problems, + // e.g. sometimes the date may be a few milliseconds earlier + // than the midnight due to precision problems in noUiSlider + return type === 'date' ? t + 3600000 : t; + }; + if (inArray(type, ['date', 'time'])) { + v[0] = strTime(v[0]); + v[1] = strTime(v[1]); + } + if (v[0] != slider_min()) v[0] *= scale; + if (v[1] != slider_max()) v[1] *= scale; + filter.val(v); + } + }); + var formatDate = function(d) { + d = scaleBack(d, scale); + if (type === 'number') return d; + if (type === 'integer') return parseInt(d); + var x = new Date(+d); + if (type === 'date') { + var pad0 = function(x) { + return ('0' + x).substr(-2, 2); + }; + return x.getUTCFullYear() + '-' + pad0(1 + x.getUTCMonth()) + + '-' + pad0(x.getUTCDate()); + } else { + return x.toISOString(); + } + }; + var opts = type === 'date' ? { step: 60 * 60 * 1000 } : + type === 'integer' ? { step: 1 } : {}; + + opts.orientation = data.vertical ? 'vertical': 'horizontal'; + opts.direction = data.vertical ? 'rtl': 'ltr'; + + filter = $x.noUiSlider($.extend({ + start: [r1, r2], + range: {min: r1, max: r2}, + connect: true + }, opts, data.filterSettings.slider)); + if (scale > 1) (function() { + var t1 = r1, t2 = r2; + var val = filter.val(); + while (val[0] > r1 || val[1] < r2) { + if (val[0] > r1) { + t1 -= val[0] - r1; + } + if (val[1] < r2) { + t2 += r2 - val[1]; + } + filter = $x.noUiSlider($.extend({ + start: [t1, t2], + range: {min: t1, max: t2}, + connect: true + }, opts, data.filterSettings.slider), true); + val = filter.val(); + } + r1 = t1; r2 = t2; + })(); + // format with active column renderer, if defined + var colDef = data.options.columnDefs.find(function(def) { + return (def.targets === i || inArray(i, def.targets)) && 'render' in def; + }); + var updateSliderText = function(v1, v2) { + // we only know how to use function renderers + if (colDef && typeof colDef.render === 'function') { + var restore = function(v) { + v = scaleBack(v, scale); + return inArray(type, ['date', 'time']) ? new Date(+v) : v; + } + $span1.text(colDef.render(restore(v1), 'display')); + $span2.text(colDef.render(restore(v2), 'display')); + } else { + $span1.text(formatDate(v1)); + $span2.text(formatDate(v2)); + } + }; + updateSliderText(r1, r2); + var updateSlider = function(e) { + var val = filter.val(); + // turn off filter if in full range + $td.data('filter', val[0] > slider_min() || val[1] < slider_max()); + var v1 = formatDate(val[0]), v2 = formatDate(val[1]), ival; + if ($td.data('filter')) { + ival = v1 + ' ... ' + v2; + $input.attr('title', ival).val(ival).trigger('input'); + } else { + $input.attr('title', '').val(''); + } + updateSliderText(val[0], val[1]); + if (e.type === 'slide') return; // no searching when sliding only + if (server) { + searchColumn(i, $td.data('filter') ? ival : '').draw(); + return; + } + table.draw(); + }; + filter.on({ + set: updateSlider, + slide: updateSlider + }); + } + + // server-side processing will be handled by R (or whatever server + // language you use); the following code is only needed for client-side + // processing + if (server) { + // if a search string has been pre-set, search now + if (searchCol) $input.trigger('input').trigger('change'); + return; + } + + var customFilter = function(settings, data, dataIndex) { + // there is no way to attach a search function to a specific table, + // and we need to make sure a global search function is not applied to + // all tables (i.e. a range filter in a previous table should not be + // applied to the current table); we use the settings object to + // determine if we want to perform searching on the current table, + // since settings.sTableId will be different to different tables + if (table.settings()[0] !== settings) return true; + // no filter on this column or no need to filter this column + if (typeof filter === 'undefined' || !$td.data('filter')) return true; + + var r = filter.val(), v, r0, r1; + var i_data = function(i) { + if (!colReorderEnabled()) return i; + var order = table.colReorder.order(), k; + for (k = 0; k < order.length; ++k) if (order[k] === i) return k; + return i; // in theory it will never be here... + } + v = data[i_data(i)]; + if (type === 'number' || type === 'integer') { + v = parseFloat(v); + // how to handle NaN? currently exclude these rows + if (isNaN(v)) return(false); + r0 = parseFloat(scaleBack(r[0], scale)) + r1 = parseFloat(scaleBack(r[1], scale)); + if (v >= r0 && v <= r1) return true; + } else if (type === 'date' || type === 'time') { + v = new Date(v); + r0 = new Date(r[0] / scale); r1 = new Date(r[1] / scale); + if (v >= r0 && v <= r1) return true; + } else if (type === 'factor') { + if (r.length === 0 || inArray(v, r)) return true; + } else if (type === 'logical') { + if (r.length === 0) return true; + if (inArray(v === '' ? 'na' : v, r)) return true; + } + return false; + }; + + $.fn.dataTable.ext.search.push(customFilter); + + // search for the preset search strings if it is non-empty + if (searchCol) $input.trigger('input').trigger('change'); + + }); + + } + + // highlight search keywords + var highlight = function() { + var body = $(table.table().body()); + // removing the old highlighting first + body.unhighlight(); + + // don't highlight the "not found" row, so we get the rows using the api + if (table.rows({ filter: 'applied' }).data().length === 0) return; + // highlight global search keywords + body.highlight($.trim(table.search()).split(/\s+/)); + // then highlight keywords from individual column filters + if (filterRow) filterRow.each(function(i, td) { + var $td = $(td), type = $td.data('type'); + if (type !== 'character') return; + var $input = $td.children('div').first().children('input'); + var column = table.column(i).nodes().to$(), + val = $.trim($input.val()); + if (type !== 'character' || val === '') return; + column.highlight(val.split(/\s+/)); + }); + }; + + if (options.searchHighlight) { + table + .on('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth', highlight) + .on('destroy', function() { + // remove event handler + table.off('draw.dt.dth column-visibility.dt.dth column-reorder.dt.dth'); + }); + + // Set the option for escaping regex characters in our search string. This will be used + // for all future matching. + jQuery.fn.highlight.options.escapeRegex = (!options.search || !options.search.regex); + + // initial highlight for state saved conditions and initial states + highlight(); + } + + // run the callback function on the table instance + if (typeof data.callback === 'function') data.callback(table); + + // double click to edit the cell, row, column, or all cells + if (data.editable) table.on('dblclick.dt', 'tbody td', function(e) { + // only bring up the editor when the cell itself is dbclicked, and ignore + // other dbclick events bubbled up (e.g. from the <input>) + if (e.target !== this) return; + var target = [], immediate = false; + switch (data.editable.target) { + case 'cell': + target = [this]; + immediate = true; // edit will take effect immediately + break; + case 'row': + target = table.cells(table.cell(this).index().row, '*').nodes(); + break; + case 'column': + target = table.cells('*', table.cell(this).index().column).nodes(); + break; + case 'all': + target = table.cells().nodes(); + break; + default: + throw 'The editable parameter must be "cell", "row", "column", or "all"'; + } + var disableCols = data.editable.disable ? data.editable.disable.columns : null; + var numericCols = data.editable.numeric; + var areaCols = data.editable.area; + var dateCols = data.editable.date; + for (var i = 0; i < target.length; i++) { + (function(cell, current) { + var $cell = $(cell), html = $cell.html(); + var _cell = table.cell(cell), value = _cell.data(), index = _cell.index().column; + var $input; + if (inArray(index, numericCols)) { + $input = $('<input type="number">'); + } else if (inArray(index, areaCols)) { + $input = $('<textarea></textarea>'); + } else if (inArray(index, dateCols)) { + $input = $('<input type="date">'); + } else { + $input = $('<input type="text">'); + } + if (!immediate) { + $cell.data('input', $input).data('html', html); + $input.attr('title', 'Hit Ctrl+Enter to finish editing, or Esc to cancel'); + } + $input.val(value); + if (inArray(index, disableCols)) { + $input.attr('readonly', '').css('filter', 'invert(25%)'); + } + $cell.empty().append($input); + if (cell === current) $input.focus(); + $input.css('width', '100%'); + + if (immediate) $input.on('blur', function(e) { + var valueNew = $input.val(); + if (valueNew !== value) { + _cell.data(valueNew); + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', [cellInfo(cell)], 'DT.cellInfo', null, {priority: 'event'}); + } + // for server-side processing, users have to call replaceData() to update the table + if (!server) table.draw(false); + } else { + $cell.html(html); + } + }).on('keyup', function(e) { + // hit Escape to cancel editing + if (e.keyCode === 27) $input.trigger('blur'); + }); + + // bulk edit (row, column, or all) + if (!immediate) $input.on('keyup', function(e) { + var removeInput = function($cell, restore) { + $cell.data('input').remove(); + if (restore) $cell.html($cell.data('html')); + } + if (e.keyCode === 27) { + for (var i = 0; i < target.length; i++) { + removeInput($(target[i]), true); + } + } else if (e.keyCode === 13 && e.ctrlKey) { + // Ctrl + Enter + var cell, $cell, _cell, cellData = []; + for (var i = 0; i < target.length; i++) { + cell = target[i]; $cell = $(cell); _cell = table.cell(cell); + _cell.data($cell.data('input').val()); + HTMLWidgets.shinyMode && cellData.push(cellInfo(cell)); + removeInput($cell, false); + } + if (HTMLWidgets.shinyMode) { + changeInput('cell_edit', cellData, 'DT.cellInfo', null, {priority: "event"}); + } + if (!server) table.draw(false); + } + }); + })(target[i], this); + } + }); + + // interaction with shiny + if (!HTMLWidgets.shinyMode && !crosstalkOptions.group) return; + + var methods = {}; + var shinyData = {}; + + methods.updateCaption = function(caption) { + if (!caption) return; + $table.children('caption').replaceWith(caption); + } + + // register clear functions to remove input values when the table is removed + instance.clearInputs = {}; + + var changeInput = function(id, value, type, noCrosstalk, opts) { + var event = id; + id = el.id + '_' + id; + if (type) id = id + ':' + type; + // do not update if the new value is the same as old value + if (event !== 'cell_edit' && !/_clicked$/.test(event) && shinyData.hasOwnProperty(id) && shinyData[id] === JSON.stringify(value)) + return; + shinyData[id] = JSON.stringify(value); + if (HTMLWidgets.shinyMode && Shiny.setInputValue) { + Shiny.setInputValue(id, value, opts); + if (!instance.clearInputs[id]) instance.clearInputs[id] = function() { + Shiny.setInputValue(id, null); + } + } + + // HACK + if (event === "rows_selected" && !noCrosstalk) { + if (crosstalkOptions.group) { + var keys = crosstalkOptions.key; + var selectedKeys = null; + if (value) { + selectedKeys = []; + for (var i = 0; i < value.length; i++) { + // The value array's contents use 1-based row numbers, so we must + // convert to 0-based before indexing into the keys array. + selectedKeys.push(keys[value[i] - 1]); + } + } + instance.ctselectHandle.set(selectedKeys); + } + } + }; + + var addOne = function(x) { + return x.map(function(i) { return 1 + i; }); + }; + + var unique = function(x) { + var ux = []; + $.each(x, function(i, el){ + if ($.inArray(el, ux) === -1) ux.push(el); + }); + return ux; + } + + // change the row index of a cell + var tweakCellIndex = function(cell) { + var info = cell.index(); + // some cell may not be valid. e.g, #759 + // when using the RowGroup extension, datatables will + // generate the row label and the cells are not part of + // the data thus contain no row/col info + if (info === undefined) + return {row: null, col: null}; + if (server) { + info.row = DT_rows_current[info.row]; + } else { + info.row += 1; + } + return {row: info.row, col: info.column}; + } + + var cleanSelectedValues = function() { + changeInput('rows_selected', []); + changeInput('columns_selected', []); + changeInput('cells_selected', transposeArray2D([]), 'shiny.matrix'); + } + // #828 we should clean the selection on the server-side when the table reloads + cleanSelectedValues(); + + // a flag to indicates if select extension is initialized or not + var flagSelectExt = table.settings()[0]._select !== undefined; + // the Select extension should only be used in the client mode and + // when the selection.mode is set to none + if (data.selection.mode === 'none' && !server && flagSelectExt) { + var updateRowsSelected = function() { + var rows = table.rows({selected: true}); + var selected = []; + $.each(rows.indexes().toArray(), function(i, v) { + selected.push(v + 1); + }); + changeInput('rows_selected', selected); + } + var updateColsSelected = function() { + var columns = table.columns({selected: true}); + changeInput('columns_selected', columns.indexes().toArray()); + } + var updateCellsSelected = function() { + var cells = table.cells({selected: true}); + var selected = []; + cells.every(function() { + var row = this.index().row; + var col = this.index().column; + selected = selected.concat([[row + 1, col]]); + }); + changeInput('cells_selected', transposeArray2D(selected), 'shiny.matrix'); + } + table.on('select deselect', function(e, dt, type, indexes) { + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + }) + updateRowsSelected(); + updateColsSelected(); + updateCellsSelected(); + } + + var selMode = data.selection.mode, selTarget = data.selection.target; + var selDisable = data.selection.selectable === false; + if (inArray(selMode, ['single', 'multiple'])) { + var selClass = inArray(data.style, ['bootstrap', 'bootstrap4']) ? 'active' : 'selected'; + // selected1: row indices; selected2: column indices + var initSel = function(x) { + if (x === null || typeof x === 'boolean' || selTarget === 'cell') { + return {rows: [], cols: []}; + } else if (selTarget === 'row') { + return {rows: $.makeArray(x), cols: []}; + } else if (selTarget === 'column') { + return {rows: [], cols: $.makeArray(x)}; + } else if (selTarget === 'row+column') { + return {rows: $.makeArray(x.rows), cols: $.makeArray(x.cols)}; + } + } + var selected = data.selection.selected; + var selected1 = initSel(selected).rows, selected2 = initSel(selected).cols; + // selectable should contain either all positive or all non-positive values, not both + // positive values indicate "selectable" while non-positive values means "nonselectable" + // the assertion is performed on R side. (only column indicides could be zero which indicates + // the row name) + var selectable = data.selection.selectable; + var selectable1 = initSel(selectable).rows, selectable2 = initSel(selectable).cols; + + // After users reorder the rows or filter the table, we cannot use the table index + // directly. Instead, we need this function to find out the rows between the two clicks. + // If user filter the table again between the start click and the end click, the behavior + // would be undefined, but it should not be a problem. + var shiftSelRowsIndex = function(start, end) { + var indexes = server ? DT_rows_all : table.rows({ search: 'applied' }).indexes().toArray(); + start = indexes.indexOf(start); end = indexes.indexOf(end); + // if start is larger than end, we need to swap + if (start > end) { + var tmp = end; end = start; start = tmp; + } + return indexes.slice(start, end + 1); + } + + var serverRowIndex = function(clientRowIndex) { + return server ? DT_rows_current[clientRowIndex] : clientRowIndex + 1; + } + + // row, column, or cell selection + var lastClickedRow; + if (inArray(selTarget, ['row', 'row+column'])) { + // Get the current selected rows. It will also + // update the selected1's value based on the current row selection state + // Note we can't put this function inside selectRows() directly, + // the reason is method.selectRows() will override selected1's value but this + // function will add rows to selected1 (keep the existing selection), which is + // inconsistent with column and cell selection. + var selectedRows = function() { + var rows = table.rows('.' + selClass); + var idx = rows.indexes().toArray(); + if (!server) { + selected1 = addOne(idx); + return selected1; + } + idx = idx.map(function(i) { + return DT_rows_current[i]; + }); + selected1 = selMode === 'multiple' ? unique(selected1.concat(idx)) : idx; + return selected1; + } + // Change selected1's value based on selectable1, then refresh the row state + var onlyKeepSelectableRows = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected1 = []; + return; + } + if (selectable1.length === 0) return; + var nonselectable = selectable1[0] <= 0; + if (nonselectable) { + // should make selectable1 positive + selected1 = $(selected1).not(selectable1.map(function(i) { return -i; })).get(); + } else { + selected1 = $(selected1).filter(selectable1).get(); + } + } + // Change selected1's value based on selectable1, then + // refresh the row selection state according to values in selected1 + var selectRows = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableRows(); + table.$('tr.' + selClass).removeClass(selClass); + if (selected1.length === 0) return; + if (server) { + table.rows({page: 'current'}).every(function() { + if (inArray(DT_rows_current[this.index()], selected1)) { + $(this.node()).addClass(selClass); + } + }); + } else { + var selected0 = selected1.map(function(i) { return i - 1; }); + $(table.rows(selected0).nodes()).addClass(selClass); + } + } + table.on('mousedown.dt', 'tbody tr', function(e) { + var $this = $(this), thisRow = table.row(this); + if (selMode === 'multiple') { + if (e.shiftKey && lastClickedRow !== undefined) { + // select or de-select depends on the last clicked row's status + var flagSel = !$this.hasClass(selClass); + var crtClickedRow = serverRowIndex(thisRow.index()); + if (server) { + var rowsIndex = shiftSelRowsIndex(lastClickedRow, crtClickedRow); + // update current page's selClass + rowsIndex.map(function(i) { + var rowIndex = DT_rows_current.indexOf(i); + if (rowIndex >= 0) { + var row = table.row(rowIndex).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + } + }); + // update selected1 + if (flagSel) { + selected1 = unique(selected1.concat(rowsIndex)); + } else { + selected1 = selected1.filter(function(index) { + return !inArray(index, rowsIndex); + }); + } + } else { + // js starts from 0 + shiftSelRowsIndex(lastClickedRow - 1, crtClickedRow - 1).map(function(value) { + var row = table.row(value).nodes().to$(); + var flagRowSel = !row.hasClass(selClass); + if (flagSel === flagRowSel) row.toggleClass(selClass); + }); + } + e.preventDefault(); + } else { + $this.toggleClass(selClass); + } + } else { + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + } else { + table.$('tr.' + selClass).removeClass(selClass); + $this.addClass(selClass); + } + } + if (server && !$this.hasClass(selClass)) { + var id = DT_rows_current[thisRow.index()]; + // remove id from selected1 since its class .selected has been removed + if (inArray(id, selected1)) selected1.splice($.inArray(id, selected1), 1); + } + selectedRows(); // update selected1's value based on selClass + selectRows(false); // only keep the selectable rows + changeInput('rows_selected', selected1); + changeInput('row_last_clicked', serverRowIndex(thisRow.index()), null, null, {priority: 'event'}); + lastClickedRow = serverRowIndex(thisRow.index()); + }); + selectRows(false); // in case users have specified pre-selected rows + // restore selected rows after the table is redrawn (e.g. sort/search/page); + // client-side tables will preserve the selections automatically; for + // server-side tables, we have to *real* row indices are in `selected1` + changeInput('rows_selected', selected1); + if (server) table.on('draw.dt', function(e) { selectRows(false); }); + methods.selectRows = function(selected, ignoreSelectable) { + selected1 = $.makeArray(selected); + selectRows(ignoreSelectable); + changeInput('rows_selected', selected1); + } + } + + if (inArray(selTarget, ['column', 'row+column'])) { + if (selTarget === 'row+column') { + $(table.columns().footer()).css('cursor', 'pointer'); + } + // update selected2's value based on selectable2 + var onlyKeepSelectableCols = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected2 = []; + return; + } + if (selectable2.length === 0) return; + var nonselectable = selectable2[0] <= 0; + if (nonselectable) { + // need to make selectable2 positive + selected2 = $(selected2).not(selectable2.map(function(i) { return -i; })).get(); + } else { + selected2 = $(selected2).filter(selectable2).get(); + } + } + // update selected2 and then + // refresh the col selection state according to values in selected2 + var selectCols = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCols(); + // if selected2 is not a valide index (e.g., larger than the column number) + // table.columns(selected2) will fail and result in a blank table + // this is different from the table.rows(), where the out-of-range indexes + // doesn't affect at all + selected2 = $(selected2).filter(table.columns().indexes()).get(); + table.columns().nodes().flatten().to$().removeClass(selClass); + if (selected2.length > 0) + table.columns(selected2).nodes().flatten().to$().addClass(selClass); + } + var callback = function() { + var colIdx = selTarget === 'column' ? table.cell(this).index().column : + $.inArray(this, table.columns().footer()), + thisCol = $(table.column(colIdx).nodes()); + if (colIdx === -1) return; + if (thisCol.hasClass(selClass)) { + thisCol.removeClass(selClass); + selected2.splice($.inArray(colIdx, selected2), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + thisCol.addClass(selClass); + selected2 = selMode === 'single' ? [colIdx] : unique(selected2.concat([colIdx])); + } + selectCols(false); // update selected2 based on selectable + changeInput('columns_selected', selected2); + } + if (selTarget === 'column') { + $(table.table().body()).on('click.dt', 'td', callback); + } else { + $(table.table().footer()).on('click.dt', 'tr th', callback); + } + selectCols(false); // in case users have specified pre-selected columns + changeInput('columns_selected', selected2); + if (server) table.on('draw.dt', function(e) { selectCols(false); }); + methods.selectColumns = function(selected, ignoreSelectable) { + selected2 = $.makeArray(selected); + selectCols(ignoreSelectable); + changeInput('columns_selected', selected2); + } + } + + if (selTarget === 'cell') { + var selected3 = [], selectable3 = []; + if (selected !== null) selected3 = selected; + if (selectable !== null && typeof selectable !== 'boolean') selectable3 = selectable; + var findIndex = function(ij, sel) { + for (var i = 0; i < sel.length; i++) { + if (ij[0] === sel[i][0] && ij[1] === sel[i][1]) return i; + } + return -1; + } + // Change selected3's value based on selectable3, then refresh the cell state + var onlyKeepSelectableCells = function() { + if (selDisable) { // users can't select; useful when only want backend select + selected3 = []; + return; + } + if (selectable3.length === 0) return; + var nonselectable = selectable3[0][0] <= 0; + var out = []; + if (nonselectable) { + selected3.map(function(ij) { + // should make selectable3 positive + if (findIndex([-ij[0], -ij[1]], selectable3) === -1) { out.push(ij); } + }); + } else { + selected3.map(function(ij) { + if (findIndex(ij, selectable3) > -1) { out.push(ij); } + }); + } + selected3 = out; + } + // Change selected3's value based on selectable3, then + // refresh the cell selection state according to values in selected3 + var selectCells = function(ignoreSelectable) { + if (!ignoreSelectable) onlyKeepSelectableCells(); + table.$('td.' + selClass).removeClass(selClass); + if (selected3.length === 0) return; + if (server) { + table.cells({page: 'current'}).every(function() { + var info = tweakCellIndex(this); + if (findIndex([info.row, info.col], selected3) > -1) + $(this.node()).addClass(selClass); + }); + } else { + selected3.map(function(ij) { + $(table.cell(ij[0] - 1, ij[1]).node()).addClass(selClass); + }); + } + }; + table.on('click.dt', 'tbody td', function() { + var $this = $(this), info = tweakCellIndex(table.cell(this)); + if ($this.hasClass(selClass)) { + $this.removeClass(selClass); + selected3.splice(findIndex([info.row, info.col], selected3), 1); + } else { + if (selMode === 'single') $(table.cells().nodes()).removeClass(selClass); + $this.addClass(selClass); + selected3 = selMode === 'single' ? [[info.row, info.col]] : + unique(selected3.concat([[info.row, info.col]])); + } + selectCells(false); // must call this to update selected3 based on selectable3 + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + }); + selectCells(false); // in case users have specified pre-selected columns + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + + if (server) table.on('draw.dt', function(e) { selectCells(false); }); + methods.selectCells = function(selected, ignoreSelectable) { + selected3 = selected ? selected : []; + selectCells(ignoreSelectable); + changeInput('cells_selected', transposeArray2D(selected3), 'shiny.matrix'); + } + } + } + + // expose some table info to Shiny + var updateTableInfo = function(e, settings) { + // TODO: is anyone interested in the page info? + // changeInput('page_info', table.page.info()); + var updateRowInfo = function(id, modifier) { + var idx; + if (server) { + idx = modifier.page === 'current' ? DT_rows_current : DT_rows_all; + } else { + var rows = table.rows($.extend({ + search: 'applied', + page: 'all' + }, modifier)); + idx = addOne(rows.indexes().toArray()); + } + changeInput('rows' + '_' + id, idx); + }; + updateRowInfo('current', {page: 'current'}); + updateRowInfo('all', {}); + } + table.on('draw.dt', updateTableInfo); + updateTableInfo(); + + // state info + table.on('draw.dt column-visibility.dt', function() { + changeInput('state', table.state()); + }); + changeInput('state', table.state()); + + // search info + var updateSearchInfo = function() { + changeInput('search', table.search()); + if (filterRow) changeInput('search_columns', filterRow.toArray().map(function(td) { + return $(td).find('input').first().val(); + })); + } + table.on('draw.dt', updateSearchInfo); + updateSearchInfo(); + + var cellInfo = function(thiz) { + var info = tweakCellIndex(table.cell(thiz)); + info.value = table.cell(thiz).data(); + return info; + } + // the current cell clicked on + table.on('click.dt', 'tbody td', function() { + changeInput('cell_clicked', cellInfo(this), null, null, {priority: 'event'}); + }) + changeInput('cell_clicked', {}); + + // do not trigger table selection when clicking on links unless they have classes + table.on('mousedown.dt', 'tbody td a', function(e) { + if (this.className === '') e.stopPropagation(); + }); + + methods.addRow = function(data, rowname, resetPaging) { + var n = table.columns().indexes().length, d = n - data.length; + if (d === 1) { + data = rowname.concat(data) + } else if (d !== 0) { + console.log(data); + console.log(table.columns().indexes()); + throw 'New data must be of the same length as current data (' + n + ')'; + }; + table.row.add(data).draw(resetPaging); + } + + methods.updateSearch = function(keywords) { + if (keywords.global !== null) + $(table.table().container()).find('input[type=search]').first() + .val(keywords.global).trigger('input'); + var columns = keywords.columns; + if (!filterRow || columns === null) return; + filterRow.toArray().map(function(td, i) { + var v = typeof columns === 'string' ? columns : columns[i]; + if (typeof v === 'undefined') { + console.log('The search keyword for column ' + i + ' is undefined') + return; + } + // Update column search string and values on linked filter widgets. + // 'input' for factor and char filters, 'change' for numeric filters. + $(td).find('input').first().val(v).trigger('input', [true]).trigger('change'); + }); + table.draw(); + } + + methods.hideCols = function(hide, reset) { + if (reset) table.columns().visible(true, false); + table.columns(hide).visible(false); + } + + methods.showCols = function(show, reset) { + if (reset) table.columns().visible(false, false); + table.columns(show).visible(true); + } + + methods.colReorder = function(order, origOrder) { + table.colReorder.order(order, origOrder); + } + + methods.selectPage = function(page) { + if (table.page.info().pages < page || page < 1) { + throw 'Selected page is out of range'; + }; + table.page(page - 1).draw(false); + } + + methods.reloadData = function(resetPaging, clearSelection) { + // empty selections first if necessary + if (methods.selectRows && inArray('row', clearSelection)) methods.selectRows([]); + if (methods.selectColumns && inArray('column', clearSelection)) methods.selectColumns([]); + if (methods.selectCells && inArray('cell', clearSelection)) methods.selectCells([]); + table.ajax.reload(null, resetPaging); + } + + // update table filters (set new limits of sliders) + methods.updateFilters = function(newProps) { + // loop through each filter in the filter row + filterRow.each(function(i, td) { + var k = i; + if (filterRow.length > newProps.length) { + if (i === 0) return; // first column is row names + k = i - 1; + } + // Update the filters to reflect the updated data. + // Allow "falsy" (e.g. NULL) to signify a no-op. + if (newProps[k]) { + setFilterProps(td, newProps[k]); + } + }); + }; + + table.shinyMethods = methods; + }, + resize: function(el, width, height, instance) { + if (instance.data) this.renderValue(el, instance.data, instance); + + // dynamically adjust height if fillContainer = TRUE + if (instance.fillContainer) + this.fillAvailableHeight(el, height); + + this.adjustWidth(el); + }, + + // dynamically set the scroll body to fill available height + // (used with fillContainer = TRUE) + fillAvailableHeight: function(el, availableHeight) { + + // see how much of the table is occupied by header/footer elements + // and use that to compute a target scroll body height + var dtWrapper = $(el).find('div.dataTables_wrapper'); + var dtScrollBody = $(el).find($('div.dataTables_scrollBody')); + var framingHeight = dtWrapper.innerHeight() - dtScrollBody.innerHeight(); + var scrollBodyHeight = availableHeight - framingHeight; + + // we need to set `max-height` to none as datatables library now sets this + // to a fixed height, disabling the ability to resize to fill the window, + // as it will be set to a fixed 100px under such circumstances, e.g., RStudio IDE, + // or FlexDashboard + // see https://github.com/rstudio/DT/issues/951#issuecomment-1026464509 + dtScrollBody.css('max-height', 'none'); + // set the height + dtScrollBody.height(scrollBodyHeight + 'px'); + }, + + // adjust the width of columns; remove the hard-coded widths on table and the + // scroll header when scrollX/Y are enabled + adjustWidth: function(el) { + var $el = $(el), table = $el.data('datatable'); + if (table) table.columns.adjust(); + $el.find('.dataTables_scrollHeadInner').css('width', '') + .children('table').css('margin-left', ''); + } +}); + + if (!HTMLWidgets.shinyMode) return; + + Shiny.addCustomMessageHandler('datatable-calls', function(data) { + var id = data.id; + var el = document.getElementById(id); + var table = el ? $(el).data('datatable') : null; + if (!table) { + console.log("Couldn't find table with id " + id); + return; + } + + var methods = table.shinyMethods, call = data.call; + if (methods[call.method]) { + methods[call.method].apply(table, call.args); + } else { + console.log("Unknown method " + call.method); + } + }); + +})(); diff --git a/docs/coverage/lib/datatables-css-0.0.0/datatables-crosstalk.css b/docs/coverage/lib/datatables-css-0.0.0/datatables-crosstalk.css new file mode 100644 index 00000000..bd1159c8 --- /dev/null +++ b/docs/coverage/lib/datatables-css-0.0.0/datatables-crosstalk.css @@ -0,0 +1,32 @@ +.dt-crosstalk-fade { + opacity: 0.2; +} + +html body div.DTS div.dataTables_scrollBody { + background: none; +} + + +/* +Fix https://github.com/rstudio/DT/issues/563 +If the `table.display` is set to "block" (e.g., pkgdown), the browser will display +datatable objects strangely. The search panel and the page buttons will still be +in full-width but the table body will be "compact" and shorter. +In therory, having this attributes will affect `dom="t"` +with `display: block` users. But in reality, there should be no one. +We may remove the below lines in the future if the upstream agree to have this there. +See https://github.com/DataTables/DataTablesSrc/issues/160 +*/ + +table.dataTable { + display: table; +} + + +/* +When DTOutput(fill = TRUE), it receives a .html-fill-item class (via htmltools::bindFillRole()), which effectively amounts to `flex: 1 1 auto`. That's mostly fine, but the case where `fillContainer=TRUE`+`height:auto`+`flex-basis:auto` and the container (e.g., a bslib::card()) doesn't have a defined height is a bit problematic since the table wants to fit the parent but the parent wants to fit the table, which results pretty small table height (maybe because there is a minimum height somewhere?). It seems better in this case to impose a 400px height default for the table, which we can do by setting `flex-basis` to 400px (the table is still allowed to grow/shrink when the container has an opinionated height). +*/ + +.html-fill-container > .html-fill-item.datatables { + flex-basis: 400px; +} diff --git a/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.extra.css b/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.extra.css new file mode 100644 index 00000000..b2dd141f --- /dev/null +++ b/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.extra.css @@ -0,0 +1,28 @@ +/* Selected rows/cells */ +table.dataTable tr.selected td, table.dataTable td.selected { + background-color: #b0bed9 !important; +} +/* In case of scrollX/Y or FixedHeader */ +.dataTables_scrollBody .dataTables_sizing { + visibility: hidden; +} + +/* The datatables' theme CSS file doesn't define +the color but with white background. It leads to an issue that +when the HTML's body color is set to 'white', the user can't +see the text since the background is white. One case happens in the +RStudio's IDE when inline viewing the DT table inside an Rmd file, +if the IDE theme is set to "Cobalt". + +See https://github.com/rstudio/DT/issues/447 for more info + +This fixes should have little side-effects because all the other elements +of the default theme use the #333 font color. + +TODO: The upstream may use relative colors for both the table background +and the color. It means the table can display well without this patch +then. At that time, we need to remove the below CSS attributes. +*/ +div.datatables { + color: #333; +} diff --git a/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.min.css b/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.min.css new file mode 100644 index 00000000..ad59f843 --- /dev/null +++ b/docs/coverage/lib/dt-core-1.13.6/css/jquery.dataTables.min.css @@ -0,0 +1 @@ +:root{--dt-row-selected: 13, 110, 253;--dt-row-selected-text: 255, 255, 255;--dt-row-selected-link: 9, 10, 11;--dt-row-stripe: 0, 0, 0;--dt-row-hover: 0, 0, 0;--dt-column-ordering: 0, 0, 0;--dt-html-background: white}:root.dark{--dt-html-background: rgb(33, 37, 41)}table.dataTable td.dt-control{text-align:center;cursor:pointer}table.dataTable td.dt-control:before{display:inline-block;color:rgba(0, 0, 0, 0.5);content:"â–º"}table.dataTable tr.dt-hasChild td.dt-control:before{content:"â–¼"}html.dark table.dataTable td.dt-control:before{color:rgba(255, 255, 255, 0.5)}html.dark table.dataTable tr.dt-hasChild 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\ No newline at end of file diff --git a/docs/coverage/lib/highlight.js-6.2/LICENSE b/docs/coverage/lib/highlight.js-6.2/LICENSE new file mode 100644 index 00000000..fe2f67b1 --- /dev/null +++ b/docs/coverage/lib/highlight.js-6.2/LICENSE @@ -0,0 +1,24 @@ +Copyright (c) 2006, Ivan Sagalaev +All rights reserved. +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above copyright + notice, this list of conditions and the following disclaimer in the + documentation and/or other materials provided with the distribution. + * Neither the name of highlight.js nor the names of its contributors + may be used to endorse or promote products derived from this software + without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY +EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. 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If there is no such method on + // the delegatee, but there was one on delegator before + // delegateMethod was called, then the original version + // is invoked instead. + // For example: + // + // var a = { + // method1: function() { console.log('a1'); } + // method2: function() { console.log('a2'); } + // }; + // var b = { + // method1: function() { console.log('b1'); } + // }; + // delegateMethod(a, b, "method1"); + // delegateMethod(a, b, "method2"); + // a.method1(); + // a.method2(); + // + // The output would be "b1", "a2". + function delegateMethod(delegator, delegatee, methodName) { + var inherited = delegator[methodName]; + delegator[methodName] = function() { + var target = delegatee; + var method = delegatee[methodName]; + + // The method doesn't exist on the delegatee. Instead, + // call the method on the delegator, if it exists. + if (!method) { + target = delegator; + method = inherited; + } + + if (method) { + return method.apply(target, arguments); + } + }; + } + + // Implement a vague facsimilie of jQuery's data method + function elementData(el, name, value) { + if (arguments.length == 2) { + return el["htmlwidget_data_" + name]; + } else if (arguments.length == 3) { + el["htmlwidget_data_" + name] = value; + return el; + } else { + throw new Error("Wrong number of arguments for elementData: " + + arguments.length); + } + } + + // http://stackoverflow.com/questions/3446170/escape-string-for-use-in-javascript-regex + function escapeRegExp(str) { + return str.replace(/[\-\[\]\/\{\}\(\)\*\+\?\.\\\^\$\|]/g, "\\$&"); + } + + function hasClass(el, className) { + var re = new RegExp("\\b" + escapeRegExp(className) + "\\b"); + return re.test(el.className); + } + + // elements - array (or array-like object) of HTML elements + // className - class name to test for + // include - if true, only return elements with given className; + // if false, only return elements *without* given className + function filterByClass(elements, className, include) { + var results = []; + for (var i = 0; i < elements.length; i++) { + if (hasClass(elements[i], className) == include) + results.push(elements[i]); + } + return results; + } + + function on(obj, eventName, func) { + if (obj.addEventListener) { + obj.addEventListener(eventName, func, false); + } else if (obj.attachEvent) { + obj.attachEvent(eventName, func); + } + } + + function off(obj, eventName, func) { + if (obj.removeEventListener) + obj.removeEventListener(eventName, func, false); + else if (obj.detachEvent) { + obj.detachEvent(eventName, func); + } + } + + // Translate array of values to top/right/bottom/left, as usual with + // the "padding" CSS property + // https://developer.mozilla.org/en-US/docs/Web/CSS/padding + function unpackPadding(value) { + if (typeof(value) === "number") + value = [value]; + if (value.length === 1) { + return {top: value[0], right: value[0], bottom: value[0], left: value[0]}; + } + if (value.length === 2) { + return {top: value[0], right: value[1], bottom: value[0], left: value[1]}; + } + if (value.length === 3) { + return {top: value[0], right: value[1], bottom: value[2], left: value[1]}; + } + if (value.length === 4) { + return {top: value[0], right: value[1], bottom: value[2], left: value[3]}; + } + } + + // Convert an unpacked padding object to a CSS value + function paddingToCss(paddingObj) { + return paddingObj.top + "px " + paddingObj.right + "px " + paddingObj.bottom + "px " + paddingObj.left + "px"; + } + + // Makes a number suitable for CSS + function px(x) { + if (typeof(x) === "number") + return x + "px"; + else + return x; + } + + // Retrieves runtime widget sizing information for an element. + // The return value is either null, or an object with fill, padding, + // defaultWidth, defaultHeight fields. + function sizingPolicy(el) { + var sizingEl = document.querySelector("script[data-for='" + el.id + "'][type='application/htmlwidget-sizing']"); + if (!sizingEl) + return null; + var sp = JSON.parse(sizingEl.textContent || sizingEl.text || "{}"); + if (viewerMode) { + return sp.viewer; + } else { + return sp.browser; + } + } + + // @param tasks Array of strings (or falsy value, in which case no-op). + // Each element must be a valid JavaScript expression that yields a + // function. Or, can be an array of objects with "code" and "data" + // properties; in this case, the "code" property should be a string + // of JS that's an expr that yields a function, and "data" should be + // an object that will be added as an additional argument when that + // function is called. + // @param target The object that will be "this" for each function + // execution. + // @param args Array of arguments to be passed to the functions. (The + // same arguments will be passed to all functions.) + function evalAndRun(tasks, target, args) { + if (tasks) { + forEach(tasks, function(task) { + var theseArgs = args; + if (typeof(task) === "object") { + theseArgs = theseArgs.concat([task.data]); + task = task.code; + } + var taskFunc = tryEval(task); + if (typeof(taskFunc) !== "function") { + throw new Error("Task must be a function! Source:\n" + task); + } + taskFunc.apply(target, theseArgs); + }); + } + } + + // Attempt eval() both with and without enclosing in parentheses. + // Note that enclosing coerces a function declaration into + // an expression that eval() can parse + // (otherwise, a SyntaxError is thrown) + function tryEval(code) { + var result = null; + try { + result = eval("(" + code + ")"); + } catch(error) { + if (!(error instanceof SyntaxError)) { + throw error; + } + try { + result = eval(code); + } catch(e) { + if (e instanceof SyntaxError) { + throw error; + } else { + throw e; + } + } + } + return result; + } + + function initSizing(el) { + var sizing = sizingPolicy(el); + if (!sizing) + return; + + var cel = document.getElementById("htmlwidget_container"); + if (!cel) + return; + + if (typeof(sizing.padding) !== "undefined") { + document.body.style.margin = "0"; + document.body.style.padding = paddingToCss(unpackPadding(sizing.padding)); + } + + if (sizing.fill) { + document.body.style.overflow = "hidden"; + document.body.style.width = "100%"; + document.body.style.height = "100%"; + document.documentElement.style.width = "100%"; + document.documentElement.style.height = "100%"; + cel.style.position = "absolute"; + var pad = unpackPadding(sizing.padding); + cel.style.top = pad.top + "px"; + cel.style.right = pad.right + "px"; + cel.style.bottom = pad.bottom + "px"; + cel.style.left = pad.left + "px"; + el.style.width = "100%"; + el.style.height = "100%"; + + return { + getWidth: function() { return cel.getBoundingClientRect().width; }, + getHeight: function() { return cel.getBoundingClientRect().height; } + }; + + } else { + el.style.width = px(sizing.width); + el.style.height = px(sizing.height); + + return { + getWidth: function() { return cel.getBoundingClientRect().width; }, + getHeight: function() { return cel.getBoundingClientRect().height; } + }; + } + } + + // Default implementations for methods + var defaults = { + find: function(scope) { + return querySelectorAll(scope, "." + this.name); + }, + renderError: function(el, err) { + var $el = $(el); + + this.clearError(el); + + // Add all these error classes, as Shiny does + var errClass = "shiny-output-error"; + if (err.type !== null) { + // use the classes of the error condition as CSS class names + errClass = errClass + " " + $.map(asArray(err.type), function(type) { + return errClass + "-" + type; + }).join(" "); + } + errClass = errClass + " htmlwidgets-error"; + + // Is el inline or block? If inline or inline-block, just display:none it + // and add an inline error. + var display = $el.css("display"); + $el.data("restore-display-mode", display); + + if (display === "inline" || display === "inline-block") { + $el.hide(); + if (err.message !== "") { + var errorSpan = $("<span>").addClass(errClass); + errorSpan.text(err.message); + $el.after(errorSpan); + } + } else if (display === "block") { + // If block, add an error just after the el, set visibility:none on the + // el, and position the error to be on top of the el. + // Mark it with a unique ID and CSS class so we can remove it later. + $el.css("visibility", "hidden"); + if (err.message !== "") { + var errorDiv = $("<div>").addClass(errClass).css("position", "absolute") + .css("top", el.offsetTop) + .css("left", el.offsetLeft) + // setting width can push out the page size, forcing otherwise + // unnecessary scrollbars to appear and making it impossible for + // the element to shrink; so use max-width instead + .css("maxWidth", el.offsetWidth) + .css("height", el.offsetHeight); + errorDiv.text(err.message); + $el.after(errorDiv); + + // Really dumb way to keep the size/position of the error in sync with + // the parent element as the window is resized or whatever. + var intId = setInterval(function() { + if (!errorDiv[0].parentElement) { + clearInterval(intId); + return; + } + errorDiv + .css("top", el.offsetTop) + .css("left", el.offsetLeft) + .css("maxWidth", el.offsetWidth) + .css("height", el.offsetHeight); + }, 500); + } + } + }, + clearError: function(el) { + var $el = $(el); + var display = $el.data("restore-display-mode"); + $el.data("restore-display-mode", null); + + if (display === "inline" || display === "inline-block") { + if (display) + $el.css("display", display); + $(el.nextSibling).filter(".htmlwidgets-error").remove(); + } else if (display === "block"){ + $el.css("visibility", "inherit"); + $(el.nextSibling).filter(".htmlwidgets-error").remove(); + } + }, + sizing: {} + }; + + // Called by widget bindings to register a new type of widget. The definition + // object can contain the following properties: + // - name (required) - A string indicating the binding name, which will be + // used by default as the CSS classname to look for. + // - initialize (optional) - A function(el) that will be called once per + // widget element; if a value is returned, it will be passed as the third + // value to renderValue. + // - renderValue (required) - A function(el, data, initValue) that will be + // called with data. Static contexts will cause this to be called once per + // element; Shiny apps will cause this to be called multiple times per + // element, as the data changes. + window.HTMLWidgets.widget = function(definition) { + if (!definition.name) { + throw new Error("Widget must have a name"); + } + if (!definition.type) { + throw new Error("Widget must have a type"); + } + // Currently we only support output widgets + if (definition.type !== "output") { + throw new Error("Unrecognized widget type '" + definition.type + "'"); + } + // TODO: Verify that .name is a valid CSS classname + + // Support new-style instance-bound definitions. Old-style class-bound + // definitions have one widget "object" per widget per type/class of + // widget; the renderValue and resize methods on such widget objects + // take el and instance arguments, because the widget object can't + // store them. New-style instance-bound definitions have one widget + // object per widget instance; the definition that's passed in doesn't + // provide renderValue or resize methods at all, just the single method + // factory(el, width, height) + // which returns an object that has renderValue(x) and resize(w, h). + // This enables a far more natural programming style for the widget + // author, who can store per-instance state using either OO-style + // instance fields or functional-style closure variables (I guess this + // is in contrast to what can only be called C-style pseudo-OO which is + // what we required before). + if (definition.factory) { + definition = createLegacyDefinitionAdapter(definition); + } + + if (!definition.renderValue) { + throw new Error("Widget must have a renderValue function"); + } + + // For static rendering (non-Shiny), use a simple widget registration + // scheme. We also use this scheme for Shiny apps/documents that also + // contain static widgets. + window.HTMLWidgets.widgets = window.HTMLWidgets.widgets || []; + // Merge defaults into the definition; don't mutate the original definition. + var staticBinding = extend({}, defaults, definition); + overrideMethod(staticBinding, "find", function(superfunc) { + return function(scope) { + var results = superfunc(scope); + // Filter out Shiny outputs, we only want the static kind + return filterByClass(results, "html-widget-output", false); + }; + }); + window.HTMLWidgets.widgets.push(staticBinding); + + if (shinyMode) { + // Shiny is running. Register the definition with an output binding. + // The definition itself will not be the output binding, instead + // we will make an output binding object that delegates to the + // definition. This is because we foolishly used the same method + // name (renderValue) for htmlwidgets definition and Shiny bindings + // but they actually have quite different semantics (the Shiny + // bindings receive data that includes lots of metadata that it + // strips off before calling htmlwidgets renderValue). We can't + // just ignore the difference because in some widgets it's helpful + // to call this.renderValue() from inside of resize(), and if + // we're not delegating, then that call will go to the Shiny + // version instead of the htmlwidgets version. + + // Merge defaults with definition, without mutating either. + var bindingDef = extend({}, defaults, definition); + + // This object will be our actual Shiny binding. + var shinyBinding = new Shiny.OutputBinding(); + + // With a few exceptions, we'll want to simply use the bindingDef's + // version of methods if they are available, otherwise fall back to + // Shiny's defaults. NOTE: If Shiny's output bindings gain additional + // methods in the future, and we want them to be overrideable by + // HTMLWidget binding definitions, then we'll need to add them to this + // list. + delegateMethod(shinyBinding, bindingDef, "getId"); + delegateMethod(shinyBinding, bindingDef, "onValueChange"); + delegateMethod(shinyBinding, bindingDef, "onValueError"); + delegateMethod(shinyBinding, bindingDef, "renderError"); + delegateMethod(shinyBinding, bindingDef, "clearError"); + delegateMethod(shinyBinding, bindingDef, "showProgress"); + + // The find, renderValue, and resize are handled differently, because we + // want to actually decorate the behavior of the bindingDef methods. + + shinyBinding.find = function(scope) { + var results = bindingDef.find(scope); + + // Only return elements that are Shiny outputs, not static ones + var dynamicResults = results.filter(".html-widget-output"); + + // It's possible that whatever caused Shiny to think there might be + // new dynamic outputs, also caused there to be new static outputs. + // Since there might be lots of different htmlwidgets bindings, we + // schedule execution for later--no need to staticRender multiple + // times. + if (results.length !== dynamicResults.length) + scheduleStaticRender(); + + return dynamicResults; + }; + + // Wrap renderValue to handle initialization, which unfortunately isn't + // supported natively by Shiny at the time of this writing. + + shinyBinding.renderValue = function(el, data) { + Shiny.renderDependencies(data.deps); + // Resolve strings marked as javascript literals to objects + if (!(data.evals instanceof Array)) data.evals = [data.evals]; + for (var i = 0; data.evals && i < data.evals.length; i++) { + window.HTMLWidgets.evaluateStringMember(data.x, data.evals[i]); + } + if (!bindingDef.renderOnNullValue) { + if (data.x === null) { + el.style.visibility = "hidden"; + return; + } else { + el.style.visibility = "inherit"; + } + } + if (!elementData(el, "initialized")) { + initSizing(el); + + elementData(el, "initialized", true); + if (bindingDef.initialize) { + var rect = el.getBoundingClientRect(); + var result = bindingDef.initialize(el, rect.width, rect.height); + elementData(el, "init_result", result); + } + } + bindingDef.renderValue(el, data.x, elementData(el, "init_result")); + evalAndRun(data.jsHooks.render, elementData(el, "init_result"), [el, data.x]); + }; + + // Only override resize if bindingDef implements it + if (bindingDef.resize) { + shinyBinding.resize = function(el, width, height) { + // Shiny can call resize before initialize/renderValue have been + // called, which doesn't make sense for widgets. + if (elementData(el, "initialized")) { + bindingDef.resize(el, width, height, elementData(el, "init_result")); + } + }; + } + + Shiny.outputBindings.register(shinyBinding, bindingDef.name); + } + }; + + var scheduleStaticRenderTimerId = null; + function scheduleStaticRender() { + if (!scheduleStaticRenderTimerId) { + scheduleStaticRenderTimerId = setTimeout(function() { + scheduleStaticRenderTimerId = null; + window.HTMLWidgets.staticRender(); + }, 1); + } + } + + // Render static widgets after the document finishes loading + // Statically render all elements that are of this widget's class + window.HTMLWidgets.staticRender = function() { + var bindings = window.HTMLWidgets.widgets || []; + forEach(bindings, function(binding) { + var matches = binding.find(document.documentElement); + forEach(matches, function(el) { + var sizeObj = initSizing(el, binding); + + var getSize = function(el) { + if (sizeObj) { + return {w: sizeObj.getWidth(), h: sizeObj.getHeight()} + } else { + var rect = el.getBoundingClientRect(); + return {w: rect.width, h: rect.height} + } + }; + + if (hasClass(el, "html-widget-static-bound")) + return; + el.className = el.className + " html-widget-static-bound"; + + var initResult; + if (binding.initialize) { + var size = getSize(el); + initResult = binding.initialize(el, size.w, size.h); + elementData(el, "init_result", initResult); + } + + if (binding.resize) { + var lastSize = getSize(el); + var resizeHandler = function(e) { + var size = getSize(el); + if (size.w === 0 && size.h === 0) + return; + if (size.w === lastSize.w && size.h === lastSize.h) + return; + lastSize = size; + binding.resize(el, size.w, size.h, initResult); + }; + + on(window, "resize", resizeHandler); + + // This is needed for cases where we're running in a Shiny + // app, but the widget itself is not a Shiny output, but + // rather a simple static widget. One example of this is + // an rmarkdown document that has runtime:shiny and widget + // that isn't in a render function. Shiny only knows to + // call resize handlers for Shiny outputs, not for static + // widgets, so we do it ourselves. + if (window.jQuery) { + window.jQuery(document).on( + "shown.htmlwidgets shown.bs.tab.htmlwidgets shown.bs.collapse.htmlwidgets", + resizeHandler + ); + window.jQuery(document).on( + "hidden.htmlwidgets hidden.bs.tab.htmlwidgets hidden.bs.collapse.htmlwidgets", + resizeHandler + ); + } + + // This is needed for the specific case of ioslides, which + // flips slides between display:none and display:block. + // Ideally we would not have to have ioslide-specific code + // here, but rather have ioslides raise a generic event, + // but the rmarkdown package just went to CRAN so the + // window to getting that fixed may be long. + if (window.addEventListener) { + // It's OK to limit this to window.addEventListener + // browsers because ioslides itself only supports + // such browsers. + on(document, "slideenter", resizeHandler); + on(document, "slideleave", resizeHandler); + } + } + + var scriptData = document.querySelector("script[data-for='" + el.id + "'][type='application/json']"); + if (scriptData) { + var data = JSON.parse(scriptData.textContent || scriptData.text); + // Resolve strings marked as javascript literals to objects + if (!(data.evals instanceof Array)) data.evals = [data.evals]; + for (var k = 0; data.evals && k < data.evals.length; k++) { + window.HTMLWidgets.evaluateStringMember(data.x, data.evals[k]); + } + binding.renderValue(el, data.x, initResult); + evalAndRun(data.jsHooks.render, initResult, [el, data.x]); + } + }); + }); + + invokePostRenderHandlers(); + } + + + function has_jQuery3() { + if (!window.jQuery) { + return false; + } + var $version = window.jQuery.fn.jquery; + var $major_version = parseInt($version.split(".")[0]); + return $major_version >= 3; + } + + /* + / Shiny 1.4 bumped jQuery from 1.x to 3.x which means jQuery's + / on-ready handler (i.e., $(fn)) is now asyncronous (i.e., it now + / really means $(setTimeout(fn)). + / https://jquery.com/upgrade-guide/3.0/#breaking-change-document-ready-handlers-are-now-asynchronous + / + / Since Shiny uses $() to schedule initShiny, shiny>=1.4 calls initShiny + / one tick later than it did before, which means staticRender() is + / called renderValue() earlier than (advanced) widget authors might be expecting. + / https://github.com/rstudio/shiny/issues/2630 + / + / For a concrete example, leaflet has some methods (e.g., updateBounds) + / which reference Shiny methods registered in initShiny (e.g., setInputValue). + / Since leaflet is privy to this life-cycle, it knows to use setTimeout() to + / delay execution of those methods (until Shiny methods are ready) + / https://github.com/rstudio/leaflet/blob/18ec981/javascript/src/index.js#L266-L268 + / + / Ideally widget authors wouldn't need to use this setTimeout() hack that + / leaflet uses to call Shiny methods on a staticRender(). In the long run, + / the logic initShiny should be broken up so that method registration happens + / right away, but binding happens later. + */ + function maybeStaticRenderLater() { + if (shinyMode && has_jQuery3()) { + window.jQuery(window.HTMLWidgets.staticRender); + } else { + window.HTMLWidgets.staticRender(); + } + } + + if (document.addEventListener) { + document.addEventListener("DOMContentLoaded", function() { + document.removeEventListener("DOMContentLoaded", arguments.callee, false); + maybeStaticRenderLater(); + }, false); + } else if (document.attachEvent) { + document.attachEvent("onreadystatechange", function() { + if (document.readyState === "complete") { + document.detachEvent("onreadystatechange", arguments.callee); + maybeStaticRenderLater(); + } + }); + } + + + window.HTMLWidgets.getAttachmentUrl = function(depname, key) { + // If no key, default to the first item + if (typeof(key) === "undefined") + key = 1; + + var link = document.getElementById(depname + "-" + key + "-attachment"); + if (!link) { + throw new Error("Attachment " + depname + "/" + key + " not found in document"); + } + return link.getAttribute("href"); + }; + + window.HTMLWidgets.dataframeToD3 = function(df) { + var names = []; + var length; + for (var name in df) { + if (df.hasOwnProperty(name)) + names.push(name); + if (typeof(df[name]) !== "object" || typeof(df[name].length) === "undefined") { + throw new Error("All fields must be arrays"); + } else if (typeof(length) !== "undefined" && length !== df[name].length) { + throw new Error("All fields must be arrays of the same length"); + } + length = df[name].length; + } + var results = []; + var item; + for (var row = 0; row < length; row++) { + item = {}; + for (var col = 0; col < names.length; col++) { + item[names[col]] = df[names[col]][row]; + } + results.push(item); + } + return results; + }; + + window.HTMLWidgets.transposeArray2D = function(array) { + if (array.length === 0) return array; + var newArray = array[0].map(function(col, i) { + return array.map(function(row) { + return row[i] + }) + }); + return newArray; + }; + // Split value at splitChar, but allow splitChar to be escaped + // using escapeChar. Any other characters escaped by escapeChar + // will be included as usual (including escapeChar itself). + function splitWithEscape(value, splitChar, escapeChar) { + var results = []; + var escapeMode = false; + var currentResult = ""; + for (var pos = 0; pos < value.length; pos++) { + if (!escapeMode) { + if (value[pos] === splitChar) { + results.push(currentResult); + currentResult = ""; + } else if (value[pos] === escapeChar) { + escapeMode = true; + } else { + currentResult += value[pos]; + } + } else { + currentResult += value[pos]; + escapeMode = false; + } + } + if (currentResult !== "") { + results.push(currentResult); + } + return results; + } + // Function authored by Yihui/JJ Allaire + window.HTMLWidgets.evaluateStringMember = function(o, member) { + var parts = splitWithEscape(member, '.', '\\'); + for (var i = 0, l = parts.length; i < l; i++) { + var part = parts[i]; + // part may be a character or 'numeric' member name + if (o !== null && typeof o === "object" && part in o) { + if (i == (l - 1)) { // if we are at the end of the line then evalulate + if (typeof o[part] === "string") + o[part] = tryEval(o[part]); + } else { // otherwise continue to next embedded object + o = o[part]; + } + } + } + }; + + // Retrieve the HTMLWidget instance (i.e. the return value of an + // HTMLWidget binding's initialize() or factory() function) + // associated with an element, or null if none. + window.HTMLWidgets.getInstance = function(el) { + return elementData(el, "init_result"); + }; + + // Finds the first element in the scope that matches the selector, + // and returns the HTMLWidget instance (i.e. the return value of + // an HTMLWidget binding's initialize() or factory() function) + // associated with that element, if any. If no element matches the + // selector, or the first matching element has no HTMLWidget + // instance associated with it, then null is returned. + // + // The scope argument is optional, and defaults to window.document. + window.HTMLWidgets.find = function(scope, selector) { + if (arguments.length == 1) { + selector = scope; + scope = document; + } + + var el = scope.querySelector(selector); + if (el === null) { + return null; + } else { + return window.HTMLWidgets.getInstance(el); + } + }; + + // Finds all elements in the scope that match the selector, and + // returns the HTMLWidget instances (i.e. the return values of + // an HTMLWidget binding's initialize() or factory() function) + // associated with the elements, in an array. If elements that + // match the selector don't have an associated HTMLWidget + // instance, the returned array will contain nulls. + // + // The scope argument is optional, and defaults to window.document. + window.HTMLWidgets.findAll = function(scope, selector) { + if (arguments.length == 1) { + selector = scope; + scope = document; + } + + var nodes = scope.querySelectorAll(selector); + var results = []; + for (var i = 0; i < nodes.length; i++) { + results.push(window.HTMLWidgets.getInstance(nodes[i])); + } + return results; + }; + + var postRenderHandlers = []; + function invokePostRenderHandlers() { + while (postRenderHandlers.length) { + var handler = postRenderHandlers.shift(); + if (handler) { + handler(); + } + } + } + + // Register the given callback function to be invoked after the + // next time static widgets are rendered. + window.HTMLWidgets.addPostRenderHandler = function(callback) { + postRenderHandlers.push(callback); + }; + + // Takes a new-style instance-bound definition, and returns an + // old-style class-bound definition. This saves us from having + // to rewrite all the logic in this file to accomodate both + // types of definitions. + function createLegacyDefinitionAdapter(defn) { + var result = { + name: defn.name, + type: defn.type, + initialize: function(el, width, height) { + return defn.factory(el, width, height); + }, + renderValue: function(el, x, instance) { + return instance.renderValue(x); + }, + resize: function(el, width, height, instance) { + return instance.resize(width, height); + } + }; + + if (defn.find) + result.find = defn.find; + if (defn.renderError) + result.renderError = defn.renderError; + if (defn.clearError) + result.clearError = defn.clearError; + + return result; + } +})(); diff --git a/docs/coverage/lib/jquery-3.6.0/jquery-3.6.0.js b/docs/coverage/lib/jquery-3.6.0/jquery-3.6.0.js new file mode 100644 index 00000000..fc6c299b --- /dev/null +++ b/docs/coverage/lib/jquery-3.6.0/jquery-3.6.0.js @@ -0,0 +1,10881 @@ +/*! + * jQuery JavaScript Library v3.6.0 + * https://jquery.com/ + * + * Includes Sizzle.js + * https://sizzlejs.com/ + * + * Copyright OpenJS Foundation and other contributors + * Released under the MIT license + * https://jquery.org/license + * + * Date: 2021-03-02T17:08Z + */ +( function( global, factory ) { + + "use strict"; + + if ( typeof module === "object" && typeof module.exports === "object" ) { + + // For CommonJS and CommonJS-like environments where a proper `window` + // is present, execute the factory and get jQuery. + // For environments that do not have a `window` with a `document` + // (such as Node.js), expose a factory as module.exports. + // This accentuates the need for the creation of a real `window`. + // e.g. var jQuery = require("jquery")(window); + // See ticket #14549 for more info. + module.exports = global.document ? + factory( global, true ) : + function( w ) { + if ( !w.document ) { + throw new Error( "jQuery requires a window with a document" ); + } + return factory( w ); + }; + } else { + factory( global ); + } + +// Pass this if window is not defined yet +} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { + +// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 +// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode +// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var flat = arr.flat ? function( array ) { + return arr.flat.call( array ); +} : function( array ) { + return arr.concat.apply( [], array ); +}; + + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + +var isFunction = function isFunction( obj ) { + + // Support: Chrome <=57, Firefox <=52 + // In some browsers, typeof returns "function" for HTML <object> elements + // (i.e., `typeof document.createElement( "object" ) === "function"`). + // We don't want to classify *any* DOM node as a function. + // Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5 + // Plus for old WebKit, typeof returns "function" for HTML collections + // (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756) + return typeof obj === "function" && typeof obj.nodeType !== "number" && + typeof obj.item !== "function"; + }; + + +var isWindow = function isWindow( obj ) { + return obj != null && obj === obj.window; + }; + + +var document = window.document; + + + + var preservedScriptAttributes = { + type: true, + src: true, + nonce: true, + noModule: true + }; + + function DOMEval( code, node, doc ) { + doc = doc || document; + + var i, val, + script = doc.createElement( "script" ); + + script.text = code; + if ( node ) { + for ( i in preservedScriptAttributes ) { + + // Support: Firefox 64+, Edge 18+ + // Some browsers don't support the "nonce" property on scripts. + // On the other hand, just using `getAttribute` is not enough as + // the `nonce` attribute is reset to an empty string whenever it + // becomes browsing-context connected. + // See https://github.com/whatwg/html/issues/2369 + // See https://html.spec.whatwg.org/#nonce-attributes + // The `node.getAttribute` check was added for the sake of + // `jQuery.globalEval` so that it can fake a nonce-containing node + // via an object. + val = node[ i ] || node.getAttribute && node.getAttribute( i ); + if ( val ) { + script.setAttribute( i, val ); + } + } + } + doc.head.appendChild( script ).parentNode.removeChild( script ); + } + + +function toType( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; +} +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.6.0", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + even: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return ( i + 1 ) % 2; + } ) ); + }, + + odd: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return i % 2; + } ) ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + copy = options[ name ]; + + // Prevent Object.prototype pollution + // Prevent never-ending loop + if ( name === "__proto__" || target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + src = target[ name ]; + + // Ensure proper type for the source value + if ( copyIsArray && !Array.isArray( src ) ) { + clone = []; + } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) { + clone = {}; + } else { + clone = src; + } + copyIsArray = false; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + // Evaluates a script in a provided context; falls back to the global one + // if not specified. + globalEval: function( code, options, doc ) { + DOMEval( code, { nonce: options && options.nonce }, doc ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return flat( ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), + function( _i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); + } ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = toType( obj ); + + if ( isFunction( obj ) || isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.6 + * https://sizzlejs.com/ + * + * Copyright JS Foundation and other contributors + * Released under the MIT license + * https://js.foundation/ + * + * Date: 2021-02-16 + */ +( function( window ) { +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + nonnativeSelectorCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ( {} ).hasOwnProperty, + arr = [], + pop = arr.pop, + pushNative = arr.push, + push = arr.push, + slice = arr.slice, + + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[ i ] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" + + "ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // https://www.w3.org/TR/css-syntax-3/#ident-token-diagram + identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace + + "?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + + // "Attribute values must be CSS identifiers [capture 5] + // or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + + whitespace + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + + "*" ), + rdescend = new RegExp( whitespace + "|>" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rhtml = /HTML$/i, + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ), + funescape = function( escape, nonHex ) { + var high = "0x" + escape.slice( 1 ) - 0x10000; + + return nonHex ? + + // Strip the backslash prefix from a non-hex escape sequence + nonHex : + + // Replace a hexadecimal escape sequence with the encoded Unicode code point + // Support: IE <=11+ + // For values outside the Basic Multilingual Plane (BMP), manually construct a + // surrogate pair + high < 0 ? + String.fromCharCode( high + 0x10000 ) : + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + inDisabledFieldset = addCombinator( + function( elem ) { + return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset"; + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + ( arr = slice.call( preferredDoc.childNodes ) ), + preferredDoc.childNodes + ); + + // Support: Android<4.0 + // Detect silently failing push.apply + // eslint-disable-next-line no-unused-expressions + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + pushNative.apply( target, slice.call( els ) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + + // Can't trust NodeList.length + while ( ( target[ j++ ] = els[ i++ ] ) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + setDocument( context ); + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) { + + // ID selector + if ( ( m = match[ 1 ] ) ) { + + // Document context + if ( nodeType === 9 ) { + if ( ( elem = context.getElementById( m ) ) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && ( elem = newContext.getElementById( m ) ) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[ 2 ] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( ( m = match[ 3 ] ) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !nonnativeSelectorCache[ selector + " " ] && + ( !rbuggyQSA || !rbuggyQSA.test( selector ) ) && + + // Support: IE 8 only + // Exclude object elements + ( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) { + + newSelector = selector; + newContext = context; + + // qSA considers elements outside a scoping root when evaluating child or + // descendant combinators, which is not what we want. + // In such cases, we work around the behavior by prefixing every selector in the + // list with an ID selector referencing the scope context. + // The technique has to be used as well when a leading combinator is used + // as such selectors are not recognized by querySelectorAll. + // Thanks to Andrew Dupont for this technique. + if ( nodeType === 1 && + ( rdescend.test( selector ) || rcombinators.test( selector ) ) ) { + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + + // We can use :scope instead of the ID hack if the browser + // supports it & if we're not changing the context. + if ( newContext !== context || !support.scope ) { + + // Capture the context ID, setting it first if necessary + if ( ( nid = context.getAttribute( "id" ) ) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", ( nid = expando ) ); + } + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " + + toSelector( groups[ i ] ); + } + newSelector = groups.join( "," ); + } + + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + nonnativeSelectorCache( selector, true ); + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return ( cache[ key + " " ] = value ); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement( "fieldset" ); + + try { + return !!fn( el ); + } catch ( e ) { + return false; + } finally { + + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split( "|" ), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[ i ] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( ( cur = cur.nextSibling ) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return ( name === "input" || name === "button" ) && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + inDisabledFieldset( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction( function( argument ) { + argument = +argument; + return markFunction( function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ ( j = matchIndexes[ i ] ) ] ) { + seed[ j ] = !( matches[ j ] = seed[ j ] ); + } + } + } ); + } ); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + var namespace = elem && elem.namespaceURI, + docElem = elem && ( elem.ownerDocument || elem ).documentElement; + + // Support: IE <=8 + // Assume HTML when documentElement doesn't yet exist, such as inside loading iframes + // https://bugs.jquery.com/ticket/4833 + return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" ); +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9 - 11+, Edge 12 - 18+ + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( preferredDoc != document && + ( subWindow = document.defaultView ) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + // Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only, + // Safari 4 - 5 only, Opera <=11.6 - 12.x only + // IE/Edge & older browsers don't support the :scope pseudo-class. + // Support: Safari 6.0 only + // Safari 6.0 supports :scope but it's an alias of :root there. + support.scope = assert( function( el ) { + docElem.appendChild( el ).appendChild( document.createElement( "div" ) ); + return typeof el.querySelectorAll !== "undefined" && + !el.querySelectorAll( ":scope fieldset div" ).length; + } ); + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert( function( el ) { + el.className = "i"; + return !el.getAttribute( "className" ); + } ); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert( function( el ) { + el.appendChild( document.createComment( "" ) ); + return !el.getElementsByTagName( "*" ).length; + } ); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert( function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + } ); + + // ID filter and find + if ( support.getById ) { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute( "id" ) === attrId; + }; + }; + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode( "id" ); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( ( elem = elems[ i++ ] ) ) { + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find[ "TAG" ] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) { + + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert( function( el ) { + + var input; + + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" + + "<select id='" + expando + "-\r\\' msallowcapture=''>" + + "<option selected=''></option></select>"; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll( "[selected]" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push( "~=" ); + } + + // Support: IE 11+, Edge 15 - 18+ + // IE 11/Edge don't find elements on a `[name='']` query in some cases. + // Adding a temporary attribute to the document before the selection works + // around the issue. + // Interestingly, IE 10 & older don't seem to have the issue. + input = document.createElement( "input" ); + input.setAttribute( "name", "" ); + el.appendChild( input ); + if ( !el.querySelectorAll( "[name='']" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" + + whitespace + "*(?:''|\"\")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll( ":checked" ).length ) { + rbuggyQSA.push( ":checked" ); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push( ".#.+[+~]" ); + } + + // Support: Firefox <=3.6 - 5 only + // Old Firefox doesn't throw on a badly-escaped identifier. + el.querySelectorAll( "\\\f" ); + rbuggyQSA.push( "[\\r\\n\\f]" ); + } ); + + assert( function( el ) { + el.innerHTML = "<a href='' disabled='disabled'></a>" + + "<select disabled='disabled'><option/></select>"; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement( "input" ); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll( "[name=d]" ).length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll( ":enabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll( ":disabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: Opera 10 - 11 only + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll( "*,:x" ); + rbuggyQSA.push( ",.*:" ); + } ); + } + + if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector ) ) ) ) { + + assert( function( el ) { + + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + } ); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + ) ); + } : + function( a, b ) { + if ( b ) { + while ( ( b = b.parentNode ) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + ( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) { + + // Choose the first element that is related to our preferred document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( a == document || a.ownerDocument == preferredDoc && + contains( preferredDoc, a ) ) { + return -1; + } + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( b == document || b.ownerDocument == preferredDoc && + contains( preferredDoc, b ) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + return a == document ? -1 : + b == document ? 1 : + /* eslint-enable eqeqeq */ + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( ( cur = cur.parentNode ) ) { + ap.unshift( cur ); + } + cur = b; + while ( ( cur = cur.parentNode ) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[ i ] === bp[ i ] ) { + i++; + } + + return i ? + + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[ i ], bp[ i ] ) : + + // Otherwise nodes in our document sort first + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + ap[ i ] == preferredDoc ? -1 : + bp[ i ] == preferredDoc ? 1 : + /* eslint-enable eqeqeq */ + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + setDocument( elem ); + + if ( support.matchesSelector && documentIsHTML && + !nonnativeSelectorCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch ( e ) { + nonnativeSelectorCache( expr, true ); + } + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( context.ownerDocument || context ) != document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( elem.ownerDocument || elem ) != document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return ( sel + "" ).replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + + // If no nodeType, this is expected to be an array + while ( ( node = elem[ i++ ] ) ) { + + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[ 1 ] = match[ 1 ].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[ 3 ] = ( match[ 3 ] || match[ 4 ] || + match[ 5 ] || "" ).replace( runescape, funescape ); + + if ( match[ 2 ] === "~=" ) { + match[ 3 ] = " " + match[ 3 ] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[ 1 ] = match[ 1 ].toLowerCase(); + + if ( match[ 1 ].slice( 0, 3 ) === "nth" ) { + + // nth-* requires argument + if ( !match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[ 4 ] = +( match[ 4 ] ? + match[ 5 ] + ( match[ 6 ] || 1 ) : + 2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) ); + match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" ); + + // other types prohibit arguments + } else if ( match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[ 6 ] && match[ 2 ]; + + if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[ 3 ] ) { + match[ 2 ] = match[ 4 ] || match[ 5 ] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + + // Get excess from tokenize (recursively) + ( excess = tokenize( unquoted, true ) ) && + + // advance to the next closing parenthesis + ( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) { + + // excess is a negative index + match[ 0 ] = match[ 0 ].slice( 0, excess ); + match[ 2 ] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { + return true; + } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + ( pattern = new RegExp( "(^|" + whitespace + + ")" + className + "(" + whitespace + "|$)" ) ) && classCache( + className, function( elem ) { + return pattern.test( + typeof elem.className === "string" && elem.className || + typeof elem.getAttribute !== "undefined" && + elem.getAttribute( "class" ) || + "" + ); + } ); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + /* eslint-disable max-len */ + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + /* eslint-enable max-len */ + + }; + }, + + "CHILD": function( type, what, _argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, _context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( ( node = node[ dir ] ) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( ( node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + + // Use previously-cached element index if available + if ( useCache ) { + + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + + // Use the same loop as above to seek `elem` from the start + while ( ( node = ++nodeIndex && node && node[ dir ] || + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || + ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction( function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[ i ] ); + seed[ idx ] = !( matches[ idx ] = matched[ i ] ); + } + } ) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + + // Potentially complex pseudos + "not": markFunction( function( selector ) { + + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction( function( seed, matches, _context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( ( elem = unmatched[ i ] ) ) { + seed[ i ] = !( matches[ i ] = elem ); + } + } + } ) : + function( elem, _context, xml ) { + input[ 0 ] = elem; + matcher( input, null, xml, results ); + + // Don't keep the element (issue #299) + input[ 0 ] = null; + return !results.pop(); + }; + } ), + + "has": markFunction( function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + } ), + + "contains": markFunction( function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1; + }; + } ), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + + // lang value must be a valid identifier + if ( !ridentifier.test( lang || "" ) ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( ( elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( ( elem = elem.parentNode ) && elem.nodeType === 1 ); + return false; + }; + } ), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && + ( !document.hasFocus || document.hasFocus() ) && + !!( elem.type || elem.href || ~elem.tabIndex ); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return ( nodeName === "input" && !!elem.checked ) || + ( nodeName === "option" && !!elem.selected ); + }, + + "selected": function( elem ) { + + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + // eslint-disable-next-line no-unused-expressions + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos[ "empty" ]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( ( attr = elem.getAttribute( "type" ) ) == null || + attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo( function() { + return [ 0 ]; + } ), + + "last": createPositionalPseudo( function( _matchIndexes, length ) { + return [ length - 1 ]; + } ), + + "eq": createPositionalPseudo( function( _matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + } ), + + "even": createPositionalPseudo( function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "odd": createPositionalPseudo( function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "lt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? + argument + length : + argument > length ? + length : + argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "gt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ) + } +}; + +Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || ( match = rcomma.exec( soFar ) ) ) { + if ( match ) { + + // Don't consume trailing commas as valid + soFar = soFar.slice( match[ 0 ].length ) || soFar; + } + groups.push( ( tokens = [] ) ); + } + + matched = false; + + // Combinators + if ( ( match = rcombinators.exec( soFar ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + + // Cast descendant combinators to space + type: match[ 0 ].replace( rtrim, " " ) + } ); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] || + ( match = preFilters[ type ]( match ) ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + type: type, + matches: match + } ); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[ i ].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || ( elem[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || + ( outerCache[ elem.uniqueID ] = {} ); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( ( oldCache = uniqueCache[ key ] ) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return ( newCache[ 2 ] = oldCache[ 2 ] ); + } else { + + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[ i ]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[ 0 ]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[ i ], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( ( elem = unmatched[ i ] ) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction( function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( + selector || "*", + context.nodeType ? [ context ] : context, + [] + ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( ( elem = temp[ i ] ) ) { + matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem ); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) ) { + + // Restore matcherIn since elem is not yet a final match + temp.push( ( matcherIn[ i ] = elem ) ); + } + } + postFinder( null, ( matcherOut = [] ), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) && + ( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) { + + seed[ temp ] = !( results[ temp ] = elem ); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + } ); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[ 0 ].type ], + implicitRelative = leadingRelative || Expr.relative[ " " ], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + ( checkContext = context ).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) { + matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ]; + } else { + matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[ j ].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens + .slice( 0, i - 1 ) + .concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } ) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ), + + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ), + len = elems.length; + + if ( outermost ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + outermostContext = context == document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id + for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( !context && elem.ownerDocument != document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( ( matcher = elementMatchers[ j++ ] ) ) { + if ( matcher( elem, context || document, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + + // They will have gone through all possible matchers + if ( ( elem = !matcher && elem ) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( ( matcher = setMatchers[ j++ ] ) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !( unmatched[ i ] || setMatched[ i ] ) ) { + setMatched[ i ] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[ i ] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( + selector, + matcherFromGroupMatchers( elementMatchers, setMatchers ) + ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( ( selector = compiled.selector || selector ) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[ 0 ] = match[ 0 ].slice( 0 ); + if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) { + + context = ( Expr.find[ "ID" ]( token.matches[ 0 ] + .replace( runescape, funescape ), context ) || [] )[ 0 ]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[ i ]; + + // Abort if we hit a combinator + if ( Expr.relative[ ( type = token.type ) ] ) { + break; + } + if ( ( find = Expr.find[ type ] ) ) { + + // Search, expanding context for leading sibling combinators + if ( ( seed = find( + token.matches[ 0 ].replace( runescape, funescape ), + rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) || + context + ) ) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert( function( el ) { + + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1; +} ); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert( function( el ) { + el.innerHTML = "<a href='#'></a>"; + return el.firstChild.getAttribute( "href" ) === "#"; +} ) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + } ); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert( function( el ) { + el.innerHTML = "<input/>"; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +} ) ) { + addHandle( "value", function( elem, _name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + } ); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert( function( el ) { + return el.getAttribute( "disabled" ) == null; +} ) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; + } + } ); +} + +return Sizzle; + +} )( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +} +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Filtered directly for both simple and complex selectors + return jQuery.filter( qualifier, elements, not ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over <tag> to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, _i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, _i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, _i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( elem.contentDocument != null && + + // Support: IE 11+ + // <object> elements with no `data` attribute has an object + // `contentDocument` with a `null` prototype. + getProto( elem.contentDocument ) ) { + + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && toType( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( _i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // rejected_handlers.disable + // fulfilled_handlers.disable + tuples[ 3 - i ][ 3 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock, + + // progress_handlers.lock + tuples[ 0 ][ 3 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the primary Deferred + primary = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + primary.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( primary.state() === "pending" || + isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return primary.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject ); + } + + return primary.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( toType( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, _key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; + + +// Matches dashed string for camelizing +var rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g; + +// Used by camelCase as callback to replace() +function fcamelCase( _all, letter ) { + return letter.toUpperCase(); +} + +// Convert dashed to camelCase; used by the css and data modules +// Support: IE <=9 - 11, Edge 12 - 15 +// Microsoft forgot to hump their vendor prefix (#9572) +function camelCase( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); +} +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( camelCase ); + } else { + key = camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var documentElement = document.documentElement; + + + + var isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ); + }, + composed = { composed: true }; + + // Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only + // Check attachment across shadow DOM boundaries when possible (gh-3504) + // Support: iOS 10.0-10.2 only + // Early iOS 10 versions support `attachShadow` but not `getRootNode`, + // leading to errors. We need to check for `getRootNode`. + if ( documentElement.getRootNode ) { + isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ) || + elem.getRootNode( composed ) === elem.ownerDocument; + }; + } +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + isAttached( elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, scale, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = elem.nodeType && + ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Support: Firefox <=54 + // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) + initial = initial / 2; + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + while ( maxIterations-- ) { + + // Evaluate and update our best guess (doubling guesses that zero out). + // Finish if the scale equals or crosses 1 (making the old*new product non-positive). + jQuery.style( elem, prop, initialInUnit + unit ); + if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) { + maxIterations = 0; + } + initialInUnit = initialInUnit / scale; + + } + + initialInUnit = initialInUnit * 2; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i ); + +var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i ); + + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = "<textarea>x</textarea>"; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // Support: IE <=9 only + // IE <=9 replaces <option> tags with their contents when inserted outside of + // the select element. + div.innerHTML = "<option></option>"; + support.option = !!div.lastChild; +} )(); + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting <tbody> or other required elements. + thead: [ 1, "<table>", "</table>" ], + col: [ 2, "<table><colgroup>", "</colgroup></table>" ], + tr: [ 2, "<table><tbody>", "</tbody></table>" ], + td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ], + + _default: [ 0, "", "" ] +}; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +// Support: IE <=9 only +if ( !support.option ) { + wrapMap.optgroup = wrapMap.option = [ 1, "<select multiple='multiple'>", "</select>" ]; +} + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, attached, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( toType( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + attached = isAttached( elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( attached ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +var rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 - 11+ +// focus() and blur() are asynchronous, except when they are no-op. +// So expect focus to be synchronous when the element is already active, +// and blur to be synchronous when the element is not already active. +// (focus and blur are always synchronous in other supported browsers, +// this just defines when we can count on it). +function expectSync( elem, type ) { + return ( elem === safeActiveElement() ) === ( type === "focus" ); +} + +// Support: IE <=9 only +// Accessing document.activeElement can throw unexpectedly +// https://bugs.jquery.com/ticket/13393 +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Only attach events to objects that accept data + if ( !acceptData( elem ) ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = Object.create( null ); + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( nativeEvent ), + + handlers = ( + dataPriv.get( this, "events" ) || Object.create( null ) + )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // If the event is namespaced, then each handler is only invoked if it is + // specially universal or its namespaces are a superset of the event's. + if ( !event.rnamespace || handleObj.namespace === false || + event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG <use> instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + click: { + + // Utilize native event to ensure correct state for checkable inputs + setup: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Claim the first handler + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + // dataPriv.set( el, "click", ... ) + leverageNative( el, "click", returnTrue ); + } + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Force setup before triggering a click + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + leverageNative( el, "click" ); + } + + // Return non-false to allow normal event-path propagation + return true; + }, + + // For cross-browser consistency, suppress native .click() on links + // Also prevent it if we're currently inside a leveraged native-event stack + _default: function( event ) { + var target = event.target; + return rcheckableType.test( target.type ) && + target.click && nodeName( target, "input" ) && + dataPriv.get( target, "click" ) || + nodeName( target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +// Ensure the presence of an event listener that handles manually-triggered +// synthetic events by interrupting progress until reinvoked in response to +// *native* events that it fires directly, ensuring that state changes have +// already occurred before other listeners are invoked. +function leverageNative( el, type, expectSync ) { + + // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add + if ( !expectSync ) { + if ( dataPriv.get( el, type ) === undefined ) { + jQuery.event.add( el, type, returnTrue ); + } + return; + } + + // Register the controller as a special universal handler for all event namespaces + dataPriv.set( el, type, false ); + jQuery.event.add( el, type, { + namespace: false, + handler: function( event ) { + var notAsync, result, + saved = dataPriv.get( this, type ); + + if ( ( event.isTrigger & 1 ) && this[ type ] ) { + + // Interrupt processing of the outer synthetic .trigger()ed event + // Saved data should be false in such cases, but might be a leftover capture object + // from an async native handler (gh-4350) + if ( !saved.length ) { + + // Store arguments for use when handling the inner native event + // There will always be at least one argument (an event object), so this array + // will not be confused with a leftover capture object. + saved = slice.call( arguments ); + dataPriv.set( this, type, saved ); + + // Trigger the native event and capture its result + // Support: IE <=9 - 11+ + // focus() and blur() are asynchronous + notAsync = expectSync( this, type ); + this[ type ](); + result = dataPriv.get( this, type ); + if ( saved !== result || notAsync ) { + dataPriv.set( this, type, false ); + } else { + result = {}; + } + if ( saved !== result ) { + + // Cancel the outer synthetic event + event.stopImmediatePropagation(); + event.preventDefault(); + + // Support: Chrome 86+ + // In Chrome, if an element having a focusout handler is blurred by + // clicking outside of it, it invokes the handler synchronously. If + // that handler calls `.remove()` on the element, the data is cleared, + // leaving `result` undefined. We need to guard against this. + return result && result.value; + } + + // If this is an inner synthetic event for an event with a bubbling surrogate + // (focus or blur), assume that the surrogate already propagated from triggering the + // native event and prevent that from happening again here. + // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the + // bubbling surrogate propagates *after* the non-bubbling base), but that seems + // less bad than duplication. + } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { + event.stopPropagation(); + } + + // If this is a native event triggered above, everything is now in order + // Fire an inner synthetic event with the original arguments + } else if ( saved.length ) { + + // ...and capture the result + dataPriv.set( this, type, { + value: jQuery.event.trigger( + + // Support: IE <=9 - 11+ + // Extend with the prototype to reset the above stopImmediatePropagation() + jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), + saved.slice( 1 ), + this + ) + } ); + + // Abort handling of the native event + event.stopImmediatePropagation(); + } + } + } ); +} + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || Date.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + code: true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + which: true +}, jQuery.event.addProp ); + +jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { + jQuery.event.special[ type ] = { + + // Utilize native event if possible so blur/focus sequence is correct + setup: function() { + + // Claim the first handler + // dataPriv.set( this, "focus", ... ) + // dataPriv.set( this, "blur", ... ) + leverageNative( this, type, expectSync ); + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function() { + + // Force setup before trigger + leverageNative( this, type ); + + // Return non-false to allow normal event-path propagation + return true; + }, + + // Suppress native focus or blur as it's already being fired + // in leverageNative. + _default: function() { + return true; + }, + + delegateType: delegateType + }; +} ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + // Support: IE <=10 - 11, Edge 12 - 13 only + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /<script|<style|<link/i, + + // checked="checked" or checked + rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, + rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( elem ).children( "tbody" )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { + elem.type = elem.type.slice( 5 ); + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.get( src ); + events = pdataOld.events; + + if ( events ) { + dataPriv.remove( dest, "handle events" ); + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = flat( args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + valueIsFunction = isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( valueIsFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( valueIsFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl && !node.noModule ) { + jQuery._evalUrl( node.src, { + nonce: node.nonce || node.getAttribute( "nonce" ) + }, doc ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && isAttached( node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html; + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = isAttached( elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + +var swap = function( elem, options, callback ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.call( elem ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + container.style.cssText = "position:absolute;left:-11111px;width:60px;" + + "margin-top:1px;padding:0;border:0"; + div.style.cssText = + "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + + "margin:auto;border:1px;padding:1px;" + + "width:60%;top:1%"; + documentElement.appendChild( container ).appendChild( div ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; + + // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 + // Some styles come back with percentage values, even though they shouldn't + div.style.right = "60%"; + pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; + + // Support: IE 9 - 11 only + // Detect misreporting of content dimensions for box-sizing:border-box elements + boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; + + // Support: IE 9 only + // Detect overflow:scroll screwiness (gh-3699) + // Support: Chrome <=64 + // Don't get tricked when zoom affects offsetWidth (gh-4029) + div.style.position = "absolute"; + scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + function roundPixelMeasures( measure ) { + return Math.round( parseFloat( measure ) ); + } + + var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, + reliableTrDimensionsVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + jQuery.extend( support, { + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelBoxStyles: function() { + computeStyleTests(); + return pixelBoxStylesVal; + }, + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + }, + scrollboxSize: function() { + computeStyleTests(); + return scrollboxSizeVal; + }, + + // Support: IE 9 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Behavior in IE 9 is more subtle than in newer versions & it passes + // some versions of this test; make sure not to make it pass there! + // + // Support: Firefox 70+ + // Only Firefox includes border widths + // in computed dimensions. (gh-4529) + reliableTrDimensions: function() { + var table, tr, trChild, trStyle; + if ( reliableTrDimensionsVal == null ) { + table = document.createElement( "table" ); + tr = document.createElement( "tr" ); + trChild = document.createElement( "div" ); + + table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate"; + tr.style.cssText = "border:1px solid"; + + // Support: Chrome 86+ + // Height set through cssText does not get applied. + // Computed height then comes back as 0. + tr.style.height = "1px"; + trChild.style.height = "9px"; + + // Support: Android 8 Chrome 86+ + // In our bodyBackground.html iframe, + // display for all div elements is set to "inline", + // which causes a problem only in Android 8 Chrome 86. + // Ensuring the div is display: block + // gets around this issue. + trChild.style.display = "block"; + + documentElement + .appendChild( table ) + .appendChild( tr ) + .appendChild( trChild ); + + trStyle = window.getComputedStyle( tr ); + reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) + + parseInt( trStyle.borderTopWidth, 10 ) + + parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight; + + documentElement.removeChild( table ); + } + return reliableTrDimensionsVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !isAttached( elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style, + vendorProps = {}; + +// Return a vendor-prefixed property or undefined +function vendorPropName( name ) { + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a potentially-mapped jQuery.cssProps or vendor prefixed property +function finalPropName( name ) { + var final = jQuery.cssProps[ name ] || vendorProps[ name ]; + + if ( final ) { + return final; + } + if ( name in emptyStyle ) { + return name; + } + return vendorProps[ name ] = vendorPropName( name ) || name; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }; + +function setPositiveNumber( _elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { + var i = dimension === "width" ? 1 : 0, + extra = 0, + delta = 0; + + // Adjustment may not be necessary + if ( box === ( isBorderBox ? "border" : "content" ) ) { + return 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin + if ( box === "margin" ) { + delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); + } + + // If we get here with a content-box, we're seeking "padding" or "border" or "margin" + if ( !isBorderBox ) { + + // Add padding + delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // For "border" or "margin", add border + if ( box !== "padding" ) { + delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + + // But still keep track of it otherwise + } else { + extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + + // If we get here with a border-box (content + padding + border), we're seeking "content" or + // "padding" or "margin" + } else { + + // For "content", subtract padding + if ( box === "content" ) { + delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // For "content" or "padding", subtract border + if ( box !== "margin" ) { + delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + // Account for positive content-box scroll gutter when requested by providing computedVal + if ( !isBorderBox && computedVal >= 0 ) { + + // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border + // Assuming integer scroll gutter, subtract the rest and round down + delta += Math.max( 0, Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + computedVal - + delta - + extra - + 0.5 + + // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter + // Use an explicit zero to avoid NaN (gh-3964) + ) ) || 0; + } + + return delta; +} + +function getWidthOrHeight( elem, dimension, extra ) { + + // Start with computed style + var styles = getStyles( elem ), + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). + // Fake content-box until we know it's needed to know the true value. + boxSizingNeeded = !support.boxSizingReliable() || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + valueIsBorderBox = isBorderBox, + + val = curCSS( elem, dimension, styles ), + offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); + + // Support: Firefox <=54 + // Return a confounding non-pixel value or feign ignorance, as appropriate. + if ( rnumnonpx.test( val ) ) { + if ( !extra ) { + return val; + } + val = "auto"; + } + + + // Support: IE 9 - 11 only + // Use offsetWidth/offsetHeight for when box sizing is unreliable. + // In those cases, the computed value can be trusted to be border-box. + if ( ( !support.boxSizingReliable() && isBorderBox || + + // Support: IE 10 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Interestingly, in some cases IE 9 doesn't suffer from this issue. + !support.reliableTrDimensions() && nodeName( elem, "tr" ) || + + // Fall back to offsetWidth/offsetHeight when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + val === "auto" || + + // Support: Android <=4.1 - 4.3 only + // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) + !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && + + // Make sure the element is visible & connected + elem.getClientRects().length ) { + + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Where available, offsetWidth/offsetHeight approximate border box dimensions. + // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the + // retrieved value as a content box dimension. + valueIsBorderBox = offsetProp in elem; + if ( valueIsBorderBox ) { + val = elem[ offsetProp ]; + } + } + + // Normalize "" and auto + val = parseFloat( val ) || 0; + + // Adjust for the element's box model + return ( val + + boxModelAdjustment( + elem, + dimension, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles, + + // Provide the current computed size to request scroll gutter calculation (gh-3589) + val + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "gridArea": true, + "gridColumn": true, + "gridColumnEnd": true, + "gridColumnStart": true, + "gridRow": true, + "gridRowEnd": true, + "gridRowStart": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: {}, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append + // "px" to a few hardcoded values. + if ( type === "number" && !isCustomProp ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( _i, dimension ) { + jQuery.cssHooks[ dimension ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, dimension, extra ); + } ) : + getWidthOrHeight( elem, dimension, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = getStyles( elem ), + + // Only read styles.position if the test has a chance to fail + // to avoid forcing a reflow. + scrollboxSizeBuggy = !support.scrollboxSize() && + styles.position === "absolute", + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) + boxSizingNeeded = scrollboxSizeBuggy || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + subtract = extra ? + boxModelAdjustment( + elem, + dimension, + extra, + isBorderBox, + styles + ) : + 0; + + // Account for unreliable border-box dimensions by comparing offset* to computed and + // faking a content-box to get border and padding (gh-3699) + if ( isBorderBox && scrollboxSizeBuggy ) { + subtract -= Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + parseFloat( styles[ dimension ] ) - + boxModelAdjustment( elem, dimension, "border", false, styles ) - + 0.5 + ); + } + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ dimension ] = value; + value = jQuery.css( elem, dimension ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( prefix !== "margin" ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && ( + jQuery.cssHooks[ tween.prop ] || + tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = Date.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 15 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY and Edge just mirrors + // the overflowX value there. + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + result.stop.bind( result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = Date.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +function classesToArray( value ) { + if ( Array.isArray( value ) ) { + return value; + } + if ( typeof value === "string" ) { + return value.match( rnothtmlwhite ) || []; + } + return []; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, + isValidValue = type === "string" || Array.isArray( value ); + + if ( typeof stateVal === "boolean" && isValidValue ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( isValidValue ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = classesToArray( value ); + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, valueIsFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + valueIsFunction = isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( valueIsFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +support.focusin = "onfocusin" in window; + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + stopPropagationCallback = function( e ) { + e.stopPropagation(); + }; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = lastElement = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + lastElement = cur; + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + + if ( event.isPropagationStopped() ) { + lastElement.addEventListener( type, stopPropagationCallback ); + } + + elem[ type ](); + + if ( event.isPropagationStopped() ) { + lastElement.removeEventListener( type, stopPropagationCallback ); + } + + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + + // Handle: regular nodes (via `this.ownerDocument`), window + // (via `this.document`) & document (via `this`). + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = { guid: Date.now() }; + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml, parserErrorElem; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) {} + + parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ]; + if ( !xml || parserErrorElem ) { + jQuery.error( "Invalid XML: " + ( + parserErrorElem ? + jQuery.map( parserErrorElem.childNodes, function( el ) { + return el.textContent; + } ).join( "\n" ) : + data + ) ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && toType( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + if ( a == null ) { + return ""; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ).filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ).map( function( _i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + +originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() + " " ] = + ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) + .concat( match[ 2 ] ); + } + } + match = responseHeaders[ key.toLowerCase() + " " ]; + } + return match == null ? null : match.join( ", " ); + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 15 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available and should be processed, append data to url + if ( s.data && ( s.processData || typeof s.data === "string" ) ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Use a noop converter for missing script but not if jsonp + if ( !isSuccess && + jQuery.inArray( "script", s.dataTypes ) > -1 && + jQuery.inArray( "json", s.dataTypes ) < 0 ) { + s.converters[ "text script" ] = function() {}; + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( _i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + +jQuery.ajaxPrefilter( function( s ) { + var i; + for ( i in s.headers ) { + if ( i.toLowerCase() === "content-type" ) { + s.contentType = s.headers[ i ] || ""; + } + } +} ); + + +jQuery._evalUrl = function( url, options, doc ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + + // Only evaluate the response if it is successful (gh-4126) + // dataFilter is not invoked for failure responses, so using it instead + // of the default converter is kludgy but it works. + converters: { + "text script": function() {} + }, + dataFilter: function( response ) { + jQuery.globalEval( response, options, doc ); + } + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var htmlIsFunction = isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.ontimeout = + xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain or forced-by-attrs requests + if ( s.crossDomain || s.scriptAttrs ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( "<script>" ) + .attr( s.scriptAttrs || {} ) + .prop( { charset: s.scriptCharset, src: s.url } ) + .on( "load error", callback = function( evt ) { + script.remove(); + callback = null; + if ( evt ) { + complete( evt.type === "error" ? 404 : 200, evt.type ); + } + } ); + + // Use native DOM manipulation to avoid our domManip AJAX trickery + document.head.appendChild( script[ 0 ] ); + }, + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +var oldCallbacks = [], + rjsonp = /(=)\?(?=&|$)|\?\?/; + +// Default jsonp settings +jQuery.ajaxSetup( { + jsonp: "callback", + jsonpCallback: function() { + var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce.guid++ ) ); + this[ callback ] = true; + return callback; + } +} ); + +// Detect, normalize options and install callbacks for jsonp requests +jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) { + + var callbackName, overwritten, responseContainer, + jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ? + "url" : + typeof s.data === "string" && + ( s.contentType || "" ) + .indexOf( "application/x-www-form-urlencoded" ) === 0 && + rjsonp.test( s.data ) && "data" + ); + + // Handle iff the expected data type is "jsonp" or we have a parameter to set + if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) { + + // Get callback name, remembering preexisting value associated with it + callbackName = s.jsonpCallback = isFunction( s.jsonpCallback ) ? + s.jsonpCallback() : + s.jsonpCallback; + + // Insert callback into url or form data + if ( jsonProp ) { + s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName ); + } else if ( s.jsonp !== false ) { + s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName; + } + + // Use data converter to retrieve json after script execution + s.converters[ "script json" ] = function() { + if ( !responseContainer ) { + jQuery.error( callbackName + " was not called" ); + } + return responseContainer[ 0 ]; + }; + + // Force json dataType + s.dataTypes[ 0 ] = "json"; + + // Install callback + overwritten = window[ callbackName ]; + window[ callbackName ] = function() { + responseContainer = arguments; + }; + + // Clean-up function (fires after converters) + jqXHR.always( function() { + + // If previous value didn't exist - remove it + if ( overwritten === undefined ) { + jQuery( window ).removeProp( callbackName ); + + // Otherwise restore preexisting value + } else { + window[ callbackName ] = overwritten; + } + + // Save back as free + if ( s[ callbackName ] ) { + + // Make sure that re-using the options doesn't screw things around + s.jsonpCallback = originalSettings.jsonpCallback; + + // Save the callback name for future use + oldCallbacks.push( callbackName ); + } + + // Call if it was a function and we have a response + if ( responseContainer && isFunction( overwritten ) ) { + overwritten( responseContainer[ 0 ] ); + } + + responseContainer = overwritten = undefined; + } ); + + // Delegate to script + return "script"; + } +} ); + + + + +// Support: Safari 8 only +// In Safari 8 documents created via document.implementation.createHTMLDocument +// collapse sibling forms: the second one becomes a child of the first one. +// Because of that, this security measure has to be disabled in Safari 8. +// https://bugs.webkit.org/show_bug.cgi?id=137337 +support.createHTMLDocument = ( function() { + var body = document.implementation.createHTMLDocument( "" ).body; + body.innerHTML = "<form></form><form></form>"; + return body.childNodes.length === 2; +} )(); + + +// Argument "data" should be string of html +// context (optional): If specified, the fragment will be created in this context, +// defaults to document +// keepScripts (optional): If true, will include scripts passed in the html string +jQuery.parseHTML = function( data, context, keepScripts ) { + if ( typeof data !== "string" ) { + return []; + } + if ( typeof context === "boolean" ) { + keepScripts = context; + context = false; + } + + var base, parsed, scripts; + + if ( !context ) { + + // Stop scripts or inline event handlers from being executed immediately + // by using document.implementation + if ( support.createHTMLDocument ) { + context = document.implementation.createHTMLDocument( "" ); + + // Set the base href for the created document + // so any parsed elements with URLs + // are based on the document's URL (gh-2965) + base = context.createElement( "base" ); + base.href = document.location.href; + context.head.appendChild( base ); + } else { + context = document; + } + } + + parsed = rsingleTag.exec( data ); + scripts = !keepScripts && []; + + // Single tag + if ( parsed ) { + return [ context.createElement( parsed[ 1 ] ) ]; + } + + parsed = buildFragment( [ data ], context, scripts ); + + if ( scripts && scripts.length ) { + jQuery( scripts ).remove(); + } + + return jQuery.merge( [], parsed.childNodes ); +}; + + +/** + * Load a url into a page + */ +jQuery.fn.load = function( url, params, callback ) { + var selector, type, response, + self = this, + off = url.indexOf( " " ); + + if ( off > -1 ) { + selector = stripAndCollapse( url.slice( off ) ); + url = url.slice( 0, off ); + } + + // If it's a function + if ( isFunction( params ) ) { + + // We assume that it's the callback + callback = params; + params = undefined; + + // Otherwise, build a param string + } else if ( params && typeof params === "object" ) { + type = "POST"; + } + + // If we have elements to modify, make the request + if ( self.length > 0 ) { + jQuery.ajax( { + url: url, + + // If "type" variable is undefined, then "GET" method will be used. + // Make value of this field explicit since + // user can override it through ajaxSetup method + type: type || "GET", + dataType: "html", + data: params + } ).done( function( responseText ) { + + // Save response for use in complete callback + response = arguments; + + self.html( selector ? + + // If a selector was specified, locate the right elements in a dummy div + // Exclude scripts to avoid IE 'Permission Denied' errors + jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) : + + // Otherwise use the full result + responseText ); + + // If the request succeeds, this function gets "data", "status", "jqXHR" + // but they are ignored because response was set above. + // If it fails, this function gets "jqXHR", "status", "error" + } ).always( callback && function( jqXHR, status ) { + self.each( function() { + callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] ); + } ); + } ); + } + + return this; +}; + + + + +jQuery.expr.pseudos.animated = function( elem ) { + return jQuery.grep( jQuery.timers, function( fn ) { + return elem === fn.elem; + } ).length; +}; + + + + +jQuery.offset = { + setOffset: function( elem, options, i ) { + var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition, + position = jQuery.css( elem, "position" ), + curElem = jQuery( elem ), + props = {}; + + // Set position first, in-case top/left are set even on static elem + if ( position === "static" ) { + elem.style.position = "relative"; + } + + curOffset = curElem.offset(); + curCSSTop = jQuery.css( elem, "top" ); + curCSSLeft = jQuery.css( elem, "left" ); + calculatePosition = ( position === "absolute" || position === "fixed" ) && + ( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1; + + // Need to be able to calculate position if either + // top or left is auto and position is either absolute or fixed + if ( calculatePosition ) { + curPosition = curElem.position(); + curTop = curPosition.top; + curLeft = curPosition.left; + + } else { + curTop = parseFloat( curCSSTop ) || 0; + curLeft = parseFloat( curCSSLeft ) || 0; + } + + if ( isFunction( options ) ) { + + // Use jQuery.extend here to allow modification of coordinates argument (gh-1848) + options = options.call( elem, i, jQuery.extend( {}, curOffset ) ); + } + + if ( options.top != null ) { + props.top = ( options.top - curOffset.top ) + curTop; + } + if ( options.left != null ) { + props.left = ( options.left - curOffset.left ) + curLeft; + } + + if ( "using" in options ) { + options.using.call( elem, props ); + + } else { + curElem.css( props ); + } + } +}; + +jQuery.fn.extend( { + + // offset() relates an element's border box to the document origin + offset: function( options ) { + + // Preserve chaining for setter + if ( arguments.length ) { + return options === undefined ? + this : + this.each( function( i ) { + jQuery.offset.setOffset( this, options, i ); + } ); + } + + var rect, win, + elem = this[ 0 ]; + + if ( !elem ) { + return; + } + + // Return zeros for disconnected and hidden (display: none) elements (gh-2310) + // Support: IE <=11 only + // Running getBoundingClientRect on a + // disconnected node in IE throws an error + if ( !elem.getClientRects().length ) { + return { top: 0, left: 0 }; + } + + // Get document-relative position by adding viewport scroll to viewport-relative gBCR + rect = elem.getBoundingClientRect(); + win = elem.ownerDocument.defaultView; + return { + top: rect.top + win.pageYOffset, + left: rect.left + win.pageXOffset + }; + }, + + // position() relates an element's margin box to its offset parent's padding box + // This corresponds to the behavior of CSS absolute positioning + position: function() { + if ( !this[ 0 ] ) { + return; + } + + var offsetParent, offset, doc, + elem = this[ 0 ], + parentOffset = { top: 0, left: 0 }; + + // position:fixed elements are offset from the viewport, which itself always has zero offset + if ( jQuery.css( elem, "position" ) === "fixed" ) { + + // Assume position:fixed implies availability of getBoundingClientRect + offset = elem.getBoundingClientRect(); + + } else { + offset = this.offset(); + + // Account for the *real* offset parent, which can be the document or its root element + // when a statically positioned element is identified + doc = elem.ownerDocument; + offsetParent = elem.offsetParent || doc.documentElement; + while ( offsetParent && + ( offsetParent === doc.body || offsetParent === doc.documentElement ) && + jQuery.css( offsetParent, "position" ) === "static" ) { + + offsetParent = offsetParent.parentNode; + } + if ( offsetParent && offsetParent !== elem && offsetParent.nodeType === 1 ) { + + // Incorporate borders into its offset, since they are outside its content origin + parentOffset = jQuery( offsetParent ).offset(); + parentOffset.top += jQuery.css( offsetParent, "borderTopWidth", true ); + parentOffset.left += jQuery.css( offsetParent, "borderLeftWidth", true ); + } + } + + // Subtract parent offsets and element margins + return { + top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ), + left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true ) + }; + }, + + // This method will return documentElement in the following cases: + // 1) For the element inside the iframe without offsetParent, this method will return + // documentElement of the parent window + // 2) For the hidden or detached element + // 3) For body or html element, i.e. in case of the html node - it will return itself + // + // but those exceptions were never presented as a real life use-cases + // and might be considered as more preferable results. + // + // This logic, however, is not guaranteed and can change at any point in the future + offsetParent: function() { + return this.map( function() { + var offsetParent = this.offsetParent; + + while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) { + offsetParent = offsetParent.offsetParent; + } + + return offsetParent || documentElement; + } ); + } +} ); + +// Create scrollLeft and scrollTop methods +jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) { + var top = "pageYOffset" === prop; + + jQuery.fn[ method ] = function( val ) { + return access( this, function( elem, method, val ) { + + // Coalesce documents and windows + var win; + if ( isWindow( elem ) ) { + win = elem; + } else if ( elem.nodeType === 9 ) { + win = elem.defaultView; + } + + if ( val === undefined ) { + return win ? win[ prop ] : elem[ method ]; + } + + if ( win ) { + win.scrollTo( + !top ? val : win.pageXOffset, + top ? val : win.pageYOffset + ); + + } else { + elem[ method ] = val; + } + }, method, val, arguments.length ); + }; +} ); + +// Support: Safari <=7 - 9.1, Chrome <=37 - 49 +// Add the top/left cssHooks using jQuery.fn.position +// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084 +// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347 +// getComputedStyle returns percent when specified for top/left/bottom/right; +// rather than make the css module depend on the offset module, just check for it here +jQuery.each( [ "top", "left" ], function( _i, prop ) { + jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition, + function( elem, computed ) { + if ( computed ) { + computed = curCSS( elem, prop ); + + // If curCSS returns percentage, fallback to offset + return rnumnonpx.test( computed ) ? + jQuery( elem ).position()[ prop ] + "px" : + computed; + } + } + ); +} ); + + +// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods +jQuery.each( { Height: "height", Width: "width" }, function( name, type ) { + jQuery.each( { + padding: "inner" + name, + content: type, + "": "outer" + name + }, function( defaultExtra, funcName ) { + + // Margin is only for outerHeight, outerWidth + jQuery.fn[ funcName ] = function( margin, value ) { + var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ), + extra = defaultExtra || ( margin === true || value === true ? "margin" : "border" ); + + return access( this, function( elem, type, value ) { + var doc; + + if ( isWindow( elem ) ) { + + // $( window ).outerWidth/Height return w/h including scrollbars (gh-1729) + return funcName.indexOf( "outer" ) === 0 ? + elem[ "inner" + name ] : + elem.document.documentElement[ "client" + name ]; + } + + // Get document width or height + if ( elem.nodeType === 9 ) { + doc = elem.documentElement; + + // Either scroll[Width/Height] or offset[Width/Height] or client[Width/Height], + // whichever is greatest + return Math.max( + elem.body[ "scroll" + name ], doc[ "scroll" + name ], + elem.body[ "offset" + name ], doc[ "offset" + name ], + doc[ "client" + name ] + ); + } + + return value === undefined ? + + // Get width or height on the element, requesting but not forcing parseFloat + jQuery.css( elem, type, extra ) : + + // Set width or height on the element + jQuery.style( elem, type, value, extra ); + }, type, chainable ? margin : undefined, chainable ); + }; + } ); +} ); + + +jQuery.each( [ + "ajaxStart", + "ajaxStop", + "ajaxComplete", + "ajaxError", + "ajaxSuccess", + "ajaxSend" +], function( _i, type ) { + jQuery.fn[ type ] = function( fn ) { + return this.on( type, fn ); + }; +} ); + + + + +jQuery.fn.extend( { + + bind: function( types, data, fn ) { + return this.on( types, null, data, fn ); + }, + unbind: function( types, fn ) { + return this.off( types, null, fn ); + }, + + delegate: function( selector, types, data, fn ) { + return this.on( types, selector, data, fn ); + }, + undelegate: function( selector, types, fn ) { + + // ( namespace ) or ( selector, types [, fn] ) + return arguments.length === 1 ? + this.off( selector, "**" ) : + this.off( types, selector || "**", fn ); + }, + + hover: function( fnOver, fnOut ) { + return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver ); + } +} ); + +jQuery.each( + ( "blur focus focusin focusout resize scroll click dblclick " + + "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " + + "change select submit keydown keypress keyup contextmenu" ).split( " " ), + function( _i, name ) { + + // Handle event binding + jQuery.fn[ name ] = function( data, fn ) { + return arguments.length > 0 ? + this.on( name, null, data, fn ) : + this.trigger( name ); + }; + } +); + + + + +// Support: Android <=4.0 only +// Make sure we trim BOM and NBSP +var rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g; + +// Bind a function to a context, optionally partially applying any +// arguments. +// jQuery.proxy is deprecated to promote standards (specifically Function#bind) +// However, it is not slated for removal any time soon +jQuery.proxy = function( fn, context ) { + var tmp, args, proxy; + + if ( typeof context === "string" ) { + tmp = fn[ context ]; + context = fn; + fn = tmp; + } + + // Quick check to determine if target is callable, in the spec + // this throws a TypeError, but we will just return undefined. + if ( !isFunction( fn ) ) { + return undefined; + } + + // Simulated bind + args = slice.call( arguments, 2 ); + proxy = function() { + return fn.apply( context || this, args.concat( slice.call( arguments ) ) ); + }; + + // Set the guid of unique handler to the same of original handler, so it can be removed + proxy.guid = fn.guid = fn.guid || jQuery.guid++; + + return proxy; +}; + +jQuery.holdReady = function( hold ) { + if ( hold ) { + jQuery.readyWait++; + } else { + jQuery.ready( true ); + } +}; +jQuery.isArray = Array.isArray; +jQuery.parseJSON = JSON.parse; +jQuery.nodeName = nodeName; +jQuery.isFunction = isFunction; +jQuery.isWindow = isWindow; +jQuery.camelCase = camelCase; +jQuery.type = toType; + +jQuery.now = Date.now; + +jQuery.isNumeric = function( obj ) { + + // As of jQuery 3.0, isNumeric is limited to + // strings and numbers (primitives or objects) + // that can be coerced to finite numbers (gh-2662) + var type = jQuery.type( obj ); + return ( type === "number" || type === "string" ) && + + // parseFloat NaNs numeric-cast false positives ("") + // ...but misinterprets leading-number strings, particularly hex literals ("0x...") + // subtraction forces infinities to NaN + !isNaN( obj - parseFloat( obj ) ); +}; + +jQuery.trim = function( text ) { + return text == null ? + "" : + ( text + "" ).replace( rtrim, "" ); +}; + + + +// Register as a named AMD module, since jQuery can be concatenated with other +// files that may use define, but not via a proper concatenation script that +// understands anonymous AMD modules. 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