diff options
Diffstat (limited to 'docs/dev')
178 files changed, 7032 insertions, 8343 deletions
diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index a35a255a..a7617d55 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -20,6 +20,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -32,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -42,7 +44,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -58,19 +60,28 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -80,7 +91,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -95,15 +106,15 @@ - </header><script src="FOCUS_D_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="FOCUS_D_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">Last change 31 January 2019 (rebuilt 2021-02-15)</h4> + <h4 data-toc-skip class="date">Last change 31 January 2019 (rebuilt 2022-11-24)</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.rmd"><code>vignettes/FOCUS_D.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> </div> @@ -112,207 +123,207 @@ <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></code></pre></div> -<pre><code>## name time value -## 1 parent 0 99.46 -## 2 parent 0 102.04 -## 3 parent 1 93.50 -## 4 parent 1 92.50 -## 5 parent 3 63.23 -## 6 parent 3 68.99 -## 7 parent 7 52.32 -## 8 parent 7 55.13 -## 9 parent 14 27.27 -## 10 parent 14 26.64 -## 11 parent 21 11.50 -## 12 parent 21 11.64 -## 13 parent 35 2.85 -## 14 parent 35 2.91 -## 15 parent 50 0.69 -## 16 parent 50 0.63 -## 17 parent 75 0.05 -## 18 parent 75 0.06 -## 19 parent 100 NA -## 20 parent 100 NA -## 21 parent 120 NA -## 22 parent 120 NA -## 23 m1 0 0.00 -## 24 m1 0 0.00 -## 25 m1 1 4.84 -## 26 m1 1 5.64 -## 27 m1 3 12.91 -## 28 m1 3 12.96 -## 29 m1 7 22.97 -## 30 m1 7 24.47 -## 31 m1 14 41.69 -## 32 m1 14 33.21 -## 33 m1 21 44.37 -## 34 m1 21 46.44 -## 35 m1 35 41.22 -## 36 m1 35 37.95 -## 37 m1 50 41.19 -## 38 m1 50 40.01 -## 39 m1 75 40.09 -## 40 m1 75 33.85 -## 41 m1 100 31.04 -## 42 m1 100 33.13 -## 43 m1 120 25.15 -## 44 m1 120 33.31</code></pre> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## name time value</span></span> +<span><span class="co">## 1 parent 0 99.46</span></span> +<span><span class="co">## 2 parent 0 102.04</span></span> +<span><span class="co">## 3 parent 1 93.50</span></span> +<span><span class="co">## 4 parent 1 92.50</span></span> +<span><span class="co">## 5 parent 3 63.23</span></span> +<span><span class="co">## 6 parent 3 68.99</span></span> +<span><span class="co">## 7 parent 7 52.32</span></span> +<span><span class="co">## 8 parent 7 55.13</span></span> +<span><span class="co">## 9 parent 14 27.27</span></span> +<span><span class="co">## 10 parent 14 26.64</span></span> +<span><span class="co">## 11 parent 21 11.50</span></span> +<span><span class="co">## 12 parent 21 11.64</span></span> +<span><span class="co">## 13 parent 35 2.85</span></span> +<span><span class="co">## 14 parent 35 2.91</span></span> +<span><span class="co">## 15 parent 50 0.69</span></span> +<span><span class="co">## 16 parent 50 0.63</span></span> +<span><span class="co">## 17 parent 75 0.05</span></span> +<span><span class="co">## 18 parent 75 0.06</span></span> +<span><span class="co">## 19 parent 100 NA</span></span> +<span><span class="co">## 20 parent 100 NA</span></span> +<span><span class="co">## 21 parent 120 NA</span></span> +<span><span class="co">## 22 parent 120 NA</span></span> +<span><span class="co">## 23 m1 0 0.00</span></span> +<span><span class="co">## 24 m1 0 0.00</span></span> +<span><span class="co">## 25 m1 1 4.84</span></span> +<span><span class="co">## 26 m1 1 5.64</span></span> +<span><span class="co">## 27 m1 3 12.91</span></span> +<span><span class="co">## 28 m1 3 12.96</span></span> +<span><span class="co">## 29 m1 7 22.97</span></span> +<span><span class="co">## 30 m1 7 24.47</span></span> +<span><span class="co">## 31 m1 14 41.69</span></span> +<span><span class="co">## 32 m1 14 33.21</span></span> +<span><span class="co">## 33 m1 21 44.37</span></span> +<span><span class="co">## 34 m1 21 46.44</span></span> +<span><span class="co">## 35 m1 35 41.22</span></span> +<span><span class="co">## 36 m1 35 37.95</span></span> +<span><span class="co">## 37 m1 50 41.19</span></span> +<span><span class="co">## 38 m1 50 40.01</span></span> +<span><span class="co">## 39 m1 75 40.09</span></span> +<span><span class="co">## 40 m1 75 33.85</span></span> +<span><span class="co">## 41 m1 100 31.04</span></span> +<span><span class="co">## 42 m1 100 33.13</span></span> +<span><span class="co">## 43 m1 120 25.15</span></span> +<span><span class="co">## 44 m1 120 33.31</span></span></code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></code></pre></div> -<pre><code>## parent -## "d_parent = - k_parent * parent" -## m1 -## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">SFO_SFO</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## parent </span></span> +<span><span class="co">## "d_parent = - k_parent * parent" </span></span> +<span><span class="co">## m1 </span></span> +<span><span class="co">## "d_m1 = + f_parent_to_m1 * k_parent * parent - k_m1 * m1"</span></span></code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value -## of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value</span></span> +<span><span class="co">## of zero were removed from the data</span></span></code></pre> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></code></pre></div> -<pre><code>## mkin version used for fitting: 1.0.3.9000 -## R version used for fitting: 4.0.3 -## Date of fit: Mon Feb 15 17:13:36 2021 -## Date of summary: Mon Feb 15 17:13:37 2021 -## -## Equations: -## d_parent/dt = - k_parent * parent -## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -## -## Model predictions using solution type analytical -## -## Fitted using 401 model solutions performed in 0.161 s -## -## Error model: Constant variance -## -## Error model algorithm: OLS -## -## Starting values for parameters to be optimised: -## value type -## parent_0 100.7500 state -## k_parent 0.1000 deparm -## k_m1 0.1001 deparm -## f_parent_to_m1 0.5000 deparm -## -## Starting values for the transformed parameters actually optimised: -## value lower upper -## parent_0 100.750000 -Inf Inf -## log_k_parent -2.302585 -Inf Inf -## log_k_m1 -2.301586 -Inf Inf -## f_parent_qlogis 0.000000 -Inf Inf -## -## Fixed parameter values: -## value type -## m1_0 0 state -## -## -## Warning(s): -## Observations with value of zero were removed from the data -## -## Results: -## -## AIC BIC logLik -## 204.4486 212.6365 -97.22429 -## -## Optimised, transformed parameters with symmetric confidence intervals: -## Estimate Std. Error Lower Upper -## parent_0 99.60000 1.57000 96.4000 102.8000 -## log_k_parent -2.31600 0.04087 -2.3990 -2.2330 -## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770 -## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395 -## sigma 3.12600 0.35850 2.3960 3.8550 -## -## Parameter correlation: -## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma -## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06 -## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07 -## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07 -## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06 -## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00 -## -## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. -## Estimate t value Pr(>t) Lower Upper -## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 -## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01 -## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03 -## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 -## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 -## -## FOCUS Chi2 error levels in percent: -## err.min n.optim df -## All data 6.398 4 15 -## parent 6.459 2 7 -## m1 4.690 2 8 -## -## Resulting formation fractions: -## ff -## parent_m1 0.5145 -## parent_sink 0.4855 -## -## Estimated disappearance times: -## DT50 DT90 -## parent 7.023 23.33 -## m1 131.761 437.70 -## -## Data: -## time variable observed predicted residual -## 0 parent 99.46 99.59848 -1.385e-01 -## 0 parent 102.04 99.59848 2.442e+00 -## 1 parent 93.50 90.23787 3.262e+00 -## 1 parent 92.50 90.23787 2.262e+00 -## 3 parent 63.23 74.07319 -1.084e+01 -## 3 parent 68.99 74.07319 -5.083e+00 -## 7 parent 52.32 49.91207 2.408e+00 -## 7 parent 55.13 49.91207 5.218e+00 -## 14 parent 27.27 25.01258 2.257e+00 -## 14 parent 26.64 25.01258 1.627e+00 -## 21 parent 11.50 12.53462 -1.035e+00 -## 21 parent 11.64 12.53462 -8.946e-01 -## 35 parent 2.85 3.14787 -2.979e-01 -## 35 parent 2.91 3.14787 -2.379e-01 -## 50 parent 0.69 0.71624 -2.624e-02 -## 50 parent 0.63 0.71624 -8.624e-02 -## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.382e-04 -## 1 m1 4.84 4.80296 3.704e-02 -## 1 m1 5.64 4.80296 8.370e-01 -## 3 m1 12.91 13.02400 -1.140e-01 -## 3 m1 12.96 13.02400 -6.400e-02 -## 7 m1 22.97 25.04476 -2.075e+00 -## 7 m1 24.47 25.04476 -5.748e-01 -## 14 m1 41.69 36.69003 5.000e+00 -## 14 m1 33.21 36.69003 -3.480e+00 -## 21 m1 44.37 41.65310 2.717e+00 -## 21 m1 46.44 41.65310 4.787e+00 -## 35 m1 41.22 43.31313 -2.093e+00 -## 35 m1 37.95 43.31313 -5.363e+00 -## 50 m1 41.19 41.21832 -2.832e-02 -## 50 m1 40.01 41.21832 -1.208e+00 -## 75 m1 40.09 36.44704 3.643e+00 -## 75 m1 33.85 36.44704 -2.597e+00 -## 100 m1 31.04 31.98162 -9.416e-01 -## 100 m1 33.13 31.98162 1.148e+00 -## 120 m1 25.15 28.78984 -3.640e+00 -## 120 m1 33.31 28.78984 4.520e+00</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:04 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:05 2022 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Equations:</span></span> +<span><span class="co">## d_parent/dt = - k_parent * parent</span></span> +<span><span class="co">## d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Model predictions using solution type analytical </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.152 s</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Error model: Constant variance </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Error model algorithm: OLS </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Starting values for parameters to be optimised:</span></span> +<span><span class="co">## value type</span></span> +<span><span class="co">## parent_0 100.7500 state</span></span> +<span><span class="co">## k_parent 0.1000 deparm</span></span> +<span><span class="co">## k_m1 0.1001 deparm</span></span> +<span><span class="co">## f_parent_to_m1 0.5000 deparm</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Starting values for the transformed parameters actually optimised:</span></span> +<span><span class="co">## value lower upper</span></span> +<span><span class="co">## parent_0 100.750000 -Inf Inf</span></span> +<span><span class="co">## log_k_parent -2.302585 -Inf Inf</span></span> +<span><span class="co">## log_k_m1 -2.301586 -Inf Inf</span></span> +<span><span class="co">## f_parent_qlogis 0.000000 -Inf Inf</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Fixed parameter values:</span></span> +<span><span class="co">## value type</span></span> +<span><span class="co">## m1_0 0 state</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Warning(s): </span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Results:</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## AIC BIC logLik</span></span> +<span><span class="co">## 204.4486 212.6365 -97.22429</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Optimised, transformed parameters with symmetric confidence intervals:</span></span> +<span><span class="co">## Estimate Std. Error Lower Upper</span></span> +<span><span class="co">## parent_0 99.60000 1.57000 96.4000 102.8000</span></span> +<span><span class="co">## log_k_parent -2.31600 0.04087 -2.3990 -2.2330</span></span> +<span><span class="co">## log_k_m1 -5.24700 0.13320 -5.5180 -4.9770</span></span> +<span><span class="co">## f_parent_qlogis 0.05792 0.08926 -0.1237 0.2395</span></span> +<span><span class="co">## sigma 3.12600 0.35850 2.3960 3.8550</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameter correlation:</span></span> +<span><span class="co">## parent_0 log_k_parent log_k_m1 f_parent_qlogis sigma</span></span> +<span><span class="co">## parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -1.172e-06</span></span> +<span><span class="co">## log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 -8.483e-07</span></span> +<span><span class="co">## log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 8.205e-07</span></span> +<span><span class="co">## f_parent_qlogis -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 1.305e-06</span></span> +<span><span class="co">## sigma -1.172e-06 -8.483e-07 8.205e-07 1.305e-06 1.000e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Backtransformed parameters:</span></span> +<span><span class="co">## Confidence intervals for internally transformed parameters are asymmetric.</span></span> +<span><span class="co">## t-test (unrealistically) based on the assumption of normal distribution</span></span> +<span><span class="co">## for estimators of untransformed parameters.</span></span> +<span><span class="co">## Estimate t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02</span></span> +<span><span class="co">## k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01</span></span> +<span><span class="co">## k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03</span></span> +<span><span class="co">## f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01</span></span> +<span><span class="co">## sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## FOCUS Chi2 error levels in percent:</span></span> +<span><span class="co">## err.min n.optim df</span></span> +<span><span class="co">## All data 6.398 4 15</span></span> +<span><span class="co">## parent 6.459 2 7</span></span> +<span><span class="co">## m1 4.690 2 8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Resulting formation fractions:</span></span> +<span><span class="co">## ff</span></span> +<span><span class="co">## parent_m1 0.5145</span></span> +<span><span class="co">## parent_sink 0.4855</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Estimated disappearance times:</span></span> +<span><span class="co">## DT50 DT90</span></span> +<span><span class="co">## parent 7.023 23.33</span></span> +<span><span class="co">## m1 131.761 437.70</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Data:</span></span> +<span><span class="co">## time variable observed predicted residual</span></span> +<span><span class="co">## 0 parent 99.46 99.59848 -1.385e-01</span></span> +<span><span class="co">## 0 parent 102.04 99.59848 2.442e+00</span></span> +<span><span class="co">## 1 parent 93.50 90.23787 3.262e+00</span></span> +<span><span class="co">## 1 parent 92.50 90.23787 2.262e+00</span></span> +<span><span class="co">## 3 parent 63.23 74.07319 -1.084e+01</span></span> +<span><span class="co">## 3 parent 68.99 74.07319 -5.083e+00</span></span> +<span><span class="co">## 7 parent 52.32 49.91207 2.408e+00</span></span> +<span><span class="co">## 7 parent 55.13 49.91207 5.218e+00</span></span> +<span><span class="co">## 14 parent 27.27 25.01258 2.257e+00</span></span> +<span><span class="co">## 14 parent 26.64 25.01258 1.627e+00</span></span> +<span><span class="co">## 21 parent 11.50 12.53462 -1.035e+00</span></span> +<span><span class="co">## 21 parent 11.64 12.53462 -8.946e-01</span></span> +<span><span class="co">## 35 parent 2.85 3.14787 -2.979e-01</span></span> +<span><span class="co">## 35 parent 2.91 3.14787 -2.379e-01</span></span> +<span><span class="co">## 50 parent 0.69 0.71624 -2.624e-02</span></span> +<span><span class="co">## 50 parent 0.63 0.71624 -8.624e-02</span></span> +<span><span class="co">## 75 parent 0.05 0.06074 -1.074e-02</span></span> +<span><span class="co">## 75 parent 0.06 0.06074 -7.382e-04</span></span> +<span><span class="co">## 1 m1 4.84 4.80296 3.704e-02</span></span> +<span><span class="co">## 1 m1 5.64 4.80296 8.370e-01</span></span> +<span><span class="co">## 3 m1 12.91 13.02400 -1.140e-01</span></span> +<span><span class="co">## 3 m1 12.96 13.02400 -6.400e-02</span></span> +<span><span class="co">## 7 m1 22.97 25.04476 -2.075e+00</span></span> +<span><span class="co">## 7 m1 24.47 25.04476 -5.748e-01</span></span> +<span><span class="co">## 14 m1 41.69 36.69003 5.000e+00</span></span> +<span><span class="co">## 14 m1 33.21 36.69003 -3.480e+00</span></span> +<span><span class="co">## 21 m1 44.37 41.65310 2.717e+00</span></span> +<span><span class="co">## 21 m1 46.44 41.65310 4.787e+00</span></span> +<span><span class="co">## 35 m1 41.22 43.31313 -2.093e+00</span></span> +<span><span class="co">## 35 m1 37.95 43.31313 -5.363e+00</span></span> +<span><span class="co">## 50 m1 41.19 41.21832 -2.832e-02</span></span> +<span><span class="co">## 50 m1 40.01 41.21832 -1.208e+00</span></span> +<span><span class="co">## 75 m1 40.09 36.44704 3.643e+00</span></span> +<span><span class="co">## 75 m1 33.85 36.44704 -2.597e+00</span></span> +<span><span class="co">## 100 m1 31.04 31.98162 -9.416e-01</span></span> +<span><span class="co">## 100 m1 33.13 31.98162 1.148e+00</span></span> +<span><span class="co">## 120 m1 25.15 28.78984 -3.640e+00</span></span> +<span><span class="co">## 120 m1 33.31 28.78984 4.520e+00</span></span></code></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -324,11 +335,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> @@ -337,5 +350,7 @@ + + </body> </html> diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex abf26715..f0b51c1f 100644 --- a/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png Binary files differindex f4937894..f6180470 100644 --- a/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png +++ b/docs/dev/articles/FOCUS_D_files/figure-html/plot_2-1.png diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html index 43ed0f69..586a6a00 100644 --- a/docs/dev/articles/FOCUS_L.html +++ b/docs/dev/articles/FOCUS_L.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,19 +63,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -106,7 +112,7 @@ <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-09-16)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2022 (rebuilt 2022-11-24)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -132,17 +138,17 @@ <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:35 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:35 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:09 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 133 model solutions performed in 0.032 s</span></span> +<span><span class="co">## Fitted using 133 model solutions performed in 0.033 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -238,17 +244,17 @@ <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> <span><span class="co">## doubtful</span></span></code></pre> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:36 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:09 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:09 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 369 model solutions performed in 0.081 s</span></span> +<span><span class="co">## Fitted using 369 model solutions performed in 0.091 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -350,17 +356,17 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:36 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:36 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:10 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 239 model solutions performed in 0.049 s</span></span> +<span><span class="co">## Fitted using 239 model solutions performed in 0.048 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -431,10 +437,10 @@ <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:37 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:37 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:10 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:10 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -443,7 +449,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 581 model solutions performed in 0.132 s</span></span> +<span><span class="co">## Fitted using 581 model solutions performed in 0.13 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -537,10 +543,10 @@ <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:37 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:11 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:11 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -549,7 +555,7 @@ <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 376 model solutions performed in 0.079 s</span></span> +<span><span class="co">## Fitted using 376 model solutions performed in 0.078 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -650,17 +656,17 @@ <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:38 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:12 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 142 model solutions performed in 0.03 s</span></span> +<span><span class="co">## Fitted using 142 model solutions performed in 0.029 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -715,17 +721,17 @@ <span><span class="co">## parent 106 352</span></span></code></pre> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.1.2 </span></span> -<span><span class="co">## R version used for fitting: 4.2.1 </span></span> -<span><span class="co">## Date of fit: Fri Sep 16 10:31:38 2022 </span></span> -<span><span class="co">## Date of summary: Fri Sep 16 10:31:38 2022 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.2 </span></span> +<span><span class="co">## R version used for fitting: 4.2.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 24 08:12:12 2022 </span></span> +<span><span class="co">## Date of summary: Thu Nov 24 08:12:12 2022 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 224 model solutions performed in 0.045 s</span></span> +<span><span class="co">## Fitted using 224 model solutions performed in 0.044 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 395b5f7c..e04302ef 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html index 27e532af..df4df718 100644 --- a/docs/dev/articles/mkin.html +++ b/docs/dev/articles/mkin.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -112,7 +112,7 @@ <h1 data-toc-skip>Introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-16)</h4> + <h4 data-toc-skip class="date">Last change 15 February 2021 (rebuilt 2022-11-24)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> diff --git a/docs/dev/articles/twa.html b/docs/dev/articles/twa.html index 30eeb5a6..673d753a 100644 --- a/docs/dev/articles/twa.html +++ b/docs/dev/articles/twa.html @@ -20,6 +20,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -32,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -42,7 +44,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -58,19 +60,28 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -80,7 +91,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -95,15 +106,15 @@ - </header><script src="twa_files/header-attrs-2.6/header-attrs.js"></script><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="twa_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Calculation of time weighted average concentrations with mkin</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">Last change 18 September 2019 (rebuilt 2021-02-15)</h4> + <h4 data-toc-skip class="date">Last change 18 September 2019 (rebuilt 2022-11-24)</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/twa.rmd"><code>vignettes/twa.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> <div class="hidden name"><code>twa.rmd</code></div> </div> @@ -141,10 +152,10 @@ <p><span class="math display">\[f_\textrm{twa} = \frac{1}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \]</span></p> -<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p> +<p>Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the <code><a href="../reference/max_twa_parent.html">max_twa_parent()</a></code> function. If the same is needed for metabolites, the function <code><a href="https://pkgdown.jrwb.de/pfm/reference/max_twa.html" class="external-link">pfm::max_twa()</a></code> from the ‘pfm’ package can be used.</p> <div id="refs" class="references hanging-indent"> <div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> </div> @@ -158,11 +169,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> @@ -171,5 +184,7 @@ + + </body> </html> diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 694b33ca..eec1ba66 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -20,6 +20,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -32,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -42,7 +44,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -58,19 +60,28 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -80,7 +91,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -95,280 +106,283 @@ - </header><script src="FOCUS_Z_files/header-attrs-2.6/header-attrs.js"></script><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="FOCUS_Z_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Example evaluation of FOCUS dataset Z</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">Last change 16 January 2018 (rebuilt 2021-02-15)</h4> + <h4 data-toc-skip class="date">Last change 16 January 2018 (rebuilt 2022-11-24)</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/FOCUS_Z.rmd"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> </div> -<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> -<div id="the-data" class="section level1"> -<h1 class="hasAnchor"> -<a href="#the-data" class="anchor"></a>The data</h1> +<p><a href="http://www.jrwb.de" class="external-link">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke" class="external-link">Privatdozent at the University of Bremen</a></p> +<div class="section level2"> +<h2 id="the-data">The data<a class="anchor" aria-label="anchor" href="#the-data"></a> +</h2> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> -<span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span> -<span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html">data.frame</a></span><span class="op">(</span> - t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>, - <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>, - Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>, - <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>, - <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>, - <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>, - <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span> - -<span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> +<span><span class="va">LOD</span> <span class="op">=</span> <span class="fl">0.5</span></span> +<span><span class="va">FOCUS_2006_Z</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> +<span> t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="fl">1</span>, <span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">7</span>, <span class="fl">10</span>, <span class="fl">14</span>, <span class="fl">21</span>,</span> +<span> <span class="fl">42</span>, <span class="fl">61</span>, <span class="fl">96</span>, <span class="fl">124</span><span class="op">)</span>,</span> +<span> Z0 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</span> +<span> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="fl">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</span> +<span> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</span> +<span> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="cn">NA</span>, <span class="fl">0.5</span> <span class="op">*</span> <span class="va">LOD</span>, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</span> +<span> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span><span class="op">)</span><span class="op">)</span></span> +<span></span> +<span><span class="va">FOCUS_2006_Z_mkin</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">FOCUS_2006_Z</span><span class="op">)</span></span></code></pre></div> </div> -<div id="parent-and-one-metabolite" class="section level1"> -<h1 class="hasAnchor"> -<a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1> +<div class="section level2"> +<h2 id="parent-and-one-metabolite">Parent and one metabolite<a class="anchor" aria-label="anchor" href="#parent-and-one-metabolite"></a> +</h2> <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 -## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 -## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762 -## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 -## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.2a.ff</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.2a.ff</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 -## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 -## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762 -## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 -## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.2a.ff</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642</span></span> +<span><span class="co">## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600</span></span> +<span><span class="co">## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762</span></span> +<span><span class="co">## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815</span></span></code></pre> <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> <div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538 -## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593 -## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760 -## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.3</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538</span></span> +<span><span class="co">## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593</span></span> +<span><span class="co">## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760</span></span> +<span><span class="co">## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790</span></span></code></pre> <p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> </div> -<div id="metabolites-z2-and-z3" class="section level1"> -<h1 class="hasAnchor"> -<a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> +<div class="section level2"> +<h2 id="metabolites-z2-and-z3">Metabolites Z2 and Z3<a class="anchor" aria-label="anchor" href="#metabolites-z2-and-z3"></a> +</h2> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, - use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> +<span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : -## Observations with value of zero were removed from the data</code></pre> -<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge: -## false convergence (8)</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.FOCUS</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.FOCUS</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.5</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, :</span></span> +<span><span class="co">## Observations with value of zero were removed from the data</span></span></code></pre> +<pre><code><span><span class="co">## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge:</span></span> +<span><span class="co">## false convergence (8)</span></span></code></pre> <div class="sourceCode" id="cb33"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664 -## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989 -## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666 -## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872 -## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965 -## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274 -## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></code></pre></div> +<pre><code><span><span class="co">## Estimate se_notrans t value Pr(>t) Lower Upper</span></span> +<span><span class="co">## Z0_0 96.838822 1.994274 48.5584 4.0280e-42 92.826981 100.850664</span></span> +<span><span class="co">## k_Z0 2.215393 0.118458 18.7019 1.0413e-23 1.989456 2.466989</span></span> +<span><span class="co">## k_Z1 0.478305 0.028258 16.9266 6.2418e-22 0.424708 0.538666</span></span> +<span><span class="co">## k_Z2 0.451627 0.042139 10.7176 1.6314e-14 0.374339 0.544872</span></span> +<span><span class="co">## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034808 0.098965</span></span> +<span><span class="co">## f_Z2_to_Z3 0.471502 0.058351 8.0805 9.6608e-11 0.357769 0.588274</span></span> +<span><span class="co">## sigma 3.984431 0.383402 10.3923 4.5575e-14 3.213126 4.755736</span></span></code></pre> <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></code></pre></div> -<pre><code>## $ff -## Z2_Z3 Z2_sink -## 0.4715 0.5285 -## -## $distimes -## DT50 DT90 -## Z0 0.31288 1.0394 -## Z1 1.44917 4.8141 -## Z2 1.53478 5.0984 -## Z3 11.80986 39.2315</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.FOCUS</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z2_Z3 Z2_sink </span></span> +<span><span class="co">## 0.4715 0.5285 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90</span></span> +<span><span class="co">## Z0 0.31288 1.0394</span></span> +<span><span class="co">## Z1 1.44917 4.8141</span></span> +<span><span class="co">## Z2 1.53478 5.0984</span></span> +<span><span class="co">## Z3 11.80986 39.2315</span></span></code></pre> <p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> </div> -<div id="using-the-sforb-model" class="section level1"> -<h1 class="hasAnchor"> -<a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> +<div class="section level2"> +<h2 id="using-the-sforb-model">Using the SFORB model<a class="anchor" aria-label="anchor" href="#using-the-sforb-model"></a> +</h2> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> <div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.1</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></code></pre></div> -<pre><code>## NULL</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.Z.mkin.1</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">$</span><span class="va">cov.unscaled</span></span></code></pre></div> +<pre><code><span><span class="co">## NULL</span></span></code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with -## value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.3</span>, <span class="va">FOCUS_2006_Z_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with</span></span> +<span><span class="co">## value of zero were removed from the data</span></span></code></pre> <div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> <div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. -## 3$bparms.ode, : Observations with value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.4</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.4</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.3</span><span class="op">$</span><span class="va">bparms.ode</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the</span></span> +<span><span class="co">## data</span></span></code></pre> <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.4</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> <div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>, - Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>, - Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## Temporary DLL for differentials generated and loaded</code></pre> +<code class="sourceCode R"><span><span class="va">Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinmod</a></span><span class="op">(</span>Z0 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z1 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z2"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> +<span> Z2 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"Z3"</span><span class="op">)</span>,</span> +<span> Z3 <span class="op">=</span> <span class="fu"><a href="../../reference/mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFORB"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin. -## 4$bparms.ode[1:4], : Observations with value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="va">m.Z.mkin.4</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">4</span><span class="op">]</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from</span></span> +<span><span class="co">## the data</span></span></code></pre> <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>, - parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>, - k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, - fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>, - quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin. -## 5$bparms.ode[1:7], : Observations with value of zero were removed from the data</code></pre> +<code class="sourceCode R"><span><span class="va">m.Z.mkin.5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">Z.mkin.5</span>, <span class="va">FOCUS_2006_Z_mkin</span>,</span> +<span> parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">m.Z.mkin.5</span><span class="op">$</span><span class="va">bparms.ode</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span><span class="op">]</span>,</span> +<span> k_Z3_bound_free <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span> +<span> fixed_parms <span class="op">=</span> <span class="st">"k_Z3_bound_free"</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini =</span></span> +<span><span class="co">## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed</span></span> +<span><span class="co">## from the data</span></span></code></pre> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> <div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/mkinparplot.html">mkinparplot</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> <div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></code></pre></div> -<pre><code>## $ff -## Z0_free Z2_Z3 Z2_sink Z3_free -## 1.00000 0.53656 0.46344 1.00000 -## -## $SFORB -## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471322 0.0075125 0.0800069 0.0000000 -## -## $distimes -## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA -## Z1 1.5148 5.0320 NA NA NA NA NA -## Z2 1.6414 5.4526 NA NA NA NA NA -## Z3 NA NA NA NA NA 8.6636 Inf</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">m.Z.mkin.5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## $ff</span></span> +<span><span class="co">## Z0_free Z2_Z3 Z2_sink Z3_free </span></span> +<span><span class="co">## 1.00000 0.53656 0.46344 1.00000 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $SFORB</span></span> +<span><span class="co">## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g </span></span> +<span><span class="co">## 2.4471322 0.0075125 0.9519862 0.0800069 0.0000000 0.9347820 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $distimes</span></span> +<span><span class="co">## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2</span></span> +<span><span class="co">## Z0 0.3043 1.1848 0.35666 0.28325 92.266 NA NA</span></span> +<span><span class="co">## Z1 1.5148 5.0320 NA NA NA NA NA</span></span> +<span><span class="co">## Z2 1.6414 5.4526 NA NA NA NA NA</span></span> +<span><span class="co">## Z3 NA NA NA NA NA 8.6636 Inf</span></span></code></pre> <p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> </div> -<div id="references" class="section level1"> -<h1 class="hasAnchor"> -<a href="#references" class="anchor"></a>References</h1> +<div class="section level2"> +<h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> <!-- vim: set foldmethod=syntax: --> <div id="refs" class="references hanging-indent"> <div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> +<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> </div> </div> @@ -385,11 +399,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> @@ -398,5 +414,7 @@ + + </body> </html> diff --git a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex 2213c446..be652d31 100644 --- a/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ b/docs/dev/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff 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a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index b9784415..a054d4a1 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -20,6 +20,8 @@ <![endif]--> </head> <body data-spy="scroll" data-target="#toc"> + + <div class="container template-article"> <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> @@ -32,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -42,7 +44,7 @@ <a href="../../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -58,19 +60,28 @@ <a href="../../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -80,7 +91,7 @@ </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="https://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> @@ -95,908 +106,908 @@ - </header><script src="NAFTA_examples_files/header-attrs-2.6/header-attrs.js"></script><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> + </header><script src="NAFTA_examples_files/accessible-code-block-0.0.1/empty-anchor.js"></script><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> <h1 data-toc-skip>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> - <h4 class="author">Johannes Ranke</h4> + <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 class="date">26 February 2019 (rebuilt 2021-02-15)</h4> + <h4 data-toc-skip class="date">26 February 2019 (rebuilt 2022-11-24)</h4> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/master/vignettes/web_only/NAFTA_examples.rmd"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> </div> -<div id="introduction" class="section level1"> -<h1 class="hasAnchor"> -<a href="#introduction" class="anchor"></a>Introduction</h1> +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> <p>In this document, the example evaluations provided in Attachment 1 to the SOP of US EPA for using the NAFTA guidance <span class="citation">(US EPA 2015)</span> are repeated using mkin. The original evaluations reported in the attachment were performed using PestDF in version 0.8.4. Note that PestDF 0.8.13 is the version distributed at the US EPA website today (2019-02-26).</p> <p>The datasets are now distributed with the mkin package.</p> </div> -<div id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4" class="anchor"></a>Examples where DFOP did not converge with PestDF 0.8.4</h1> +<div class="section level2"> +<h2 id="examples-where-dfop-did-not-converge-with-pestdf-0-8-4">Examples where DFOP did not converge with PestDF 0.8.4<a class="anchor" aria-label="anchor" href="#examples-where-dfop-did-not-converge-with-pestdf-0-8-4"></a> +</h2> <p>In attachment 1, it is reported that the DFOP model does not converge for these datasets when PestDF 0.8.4 was used. For all four datasets, the DFOP model can be fitted with mkin (see below). The negative half-life given by PestDF 0.8.4 for these fits appears to be the result of a bug. The results for the other two models (SFO and IORE) are the same.</p> -<div id="example-on-page-5-upper-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> +<div class="section level3"> +<h3 id="example-on-page-5-upper-panel">Example on page 5, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-upper-panel"></a> +</h3> <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p5a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 465.21753 56.27506 32.06401 -## -## Critical sum of squares for checking the SFO model: -## [1] 64.4304 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.8401 4.67e-21 92.245 99.4357 -## k_parent 0.0102 3.92e-12 0.009 0.0117 -## sigma 4.8230 3.81e-06 3.214 6.4318 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 -## N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -## sigma 1.68e+00 NA 1.12e+00 2.24e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 -## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.26e-12 5.00e-01 0.0000 Inf -## g 6.47e-01 3.67e-06 0.6248 0.6677 -## sigma 1.27e+00 8.91e-06 0.8395 1.6929 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 67.7 2.25e+02 6.77e+01 -## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.59e+11 3.07e+11 -## -## Representative half-life: -## [1] 321.51</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 465.21753 56.27506 32.06401 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 64.4304</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.8401 4.67e-21 92.245 99.4357</span></span> +<span><span class="co">## k_parent 0.0102 3.92e-12 0.009 0.0117</span></span> +<span><span class="co">## sigma 4.8230 3.81e-06 3.214 6.4318</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span></span> +<span><span class="co">## N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span></span> +<span><span class="co">## sigma 1.68e+00 NA 1.12e+00 2.24e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span></span> +<span><span class="co">## k1 2.67e-02 5.05e-06 0.0243 0.0295</span></span> +<span><span class="co">## k2 2.26e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.47e-01 3.67e-06 0.6248 0.6677</span></span> +<span><span class="co">## sigma 1.27e+00 8.91e-06 0.8395 1.6929</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 67.7 2.25e+02 6.77e+01</span></span> +<span><span class="co">## IORE 58.2 1.07e+03 3.22e+02</span></span> +<span><span class="co">## DFOP 55.5 5.59e+11 3.07e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 321.51</span></span></code></pre> </div> -<div id="example-on-page-5-lower-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> +<div class="section level3"> +<h3 id="example-on-page-5-lower-panel">Example on page 5, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-5-lower-panel"></a> +</h3> <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p5b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 94.81123 10.10936 7.55871 -## -## Critical sum of squares for checking the SFO model: -## [1] 11.77879 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497 2.32e-24 94.85271 98.14155 -## k_parent 0.008 3.42e-14 0.00737 0.00869 -## sigma 2.295 1.22e-05 1.47976 3.11036 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 -## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04 -## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00 -## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 -## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 8.63e-12 5.00e-01 0.0000 Inf -## g 6.89e-01 2.92e-03 0.6626 0.7142 -## sigma 6.48e-01 2.38e-05 0.4147 0.8813 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 86.6 2.88e+02 8.66e+01 -## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.32e+11 8.04e+10 -## -## Representative half-life: -## [1] 215.87</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p5b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 94.81123 10.10936 7.55871 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 11.77879</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.497 2.32e-24 94.85271 98.14155</span></span> +<span><span class="co">## k_parent 0.008 3.42e-14 0.00737 0.00869</span></span> +<span><span class="co">## sigma 2.295 1.22e-05 1.47976 3.11036</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01</span></span> +<span><span class="co">## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04</span></span> +<span><span class="co">## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00</span></span> +<span><span class="co">## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.84e+01 1.24e-27 97.8078 98.9187</span></span> +<span><span class="co">## k1 1.55e-02 4.10e-04 0.0143 0.0167</span></span> +<span><span class="co">## k2 8.63e-12 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.89e-01 2.92e-03 0.6626 0.7142</span></span> +<span><span class="co">## sigma 6.48e-01 2.38e-05 0.4147 0.8813</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.6 2.88e+02 8.66e+01</span></span> +<span><span class="co">## IORE 85.5 7.17e+02 2.16e+02</span></span> +<span><span class="co">## DFOP 83.6 1.32e+11 8.04e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 215.87</span></span></code></pre> </div> -<div id="example-on-page-6" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> +<div class="section level3"> +<h3 id="example-on-page-6">Example on page 6<a class="anchor" aria-label="anchor" href="#example-on-page-6"></a> +</h3> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p6</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p6"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 188.45361 51.00699 42.46931 -## -## Critical sum of squares for checking the SFO model: -## [1] 58.39888 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7759 7.29e-24 92.3478 97.2039 -## k_parent 0.0179 8.02e-16 0.0166 0.0194 -## sigma 3.0696 3.81e-06 2.0456 4.0936 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 97.12446 2.63e-26 95.62461 98.62431 -## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472 -## N_parent 1.49587 4.07e-13 1.33896 1.65279 -## sigma 1.59698 5.05e-06 1.06169 2.13227 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 -## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.22e-11 5.00e-01 0.0000 Inf -## g 8.61e-01 7.55e-06 0.8314 0.8867 -## sigma 1.46e+00 6.93e-06 0.9661 1.9483 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 38.6 1.28e+02 3.86e+01 -## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 1.01e+10 2.15e+10 -## -## Representative half-life: -## [1] 53.17</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p6</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 188.45361 51.00699 42.46931 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 58.39888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7759 7.29e-24 92.3478 97.2039</span></span> +<span><span class="co">## k_parent 0.0179 8.02e-16 0.0166 0.0194</span></span> +<span><span class="co">## sigma 3.0696 3.81e-06 2.0456 4.0936</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.12446 2.63e-26 95.62461 98.62431</span></span> +<span><span class="co">## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472</span></span> +<span><span class="co">## N_parent 1.49587 4.07e-13 1.33896 1.65279</span></span> +<span><span class="co">## sigma 1.59698 5.05e-06 1.06169 2.13227</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.66e+01 1.57e-25 95.3476 97.8979</span></span> +<span><span class="co">## k1 2.55e-02 7.33e-06 0.0233 0.0278</span></span> +<span><span class="co">## k2 3.22e-11 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 8.61e-01 7.55e-06 0.8314 0.8867</span></span> +<span><span class="co">## sigma 1.46e+00 6.93e-06 0.9661 1.9483</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 38.6 1.28e+02 3.86e+01</span></span> +<span><span class="co">## IORE 34.0 1.77e+02 5.32e+01</span></span> +<span><span class="co">## DFOP 34.1 1.01e+10 2.15e+10</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 53.17</span></span></code></pre> </div> -<div id="example-on-page-7" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> +<div class="section level3"> +<h3 id="example-on-page-7">Example on page 7<a class="anchor" aria-label="anchor" href="#example-on-page-7"></a> +</h3> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p7</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p7"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> <div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 3661.661 3195.030 3174.145 -## -## Critical sum of squares for checking the SFO model: -## [1] 3334.194 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.41796 4.80e-53 93.32245 99.51347 -## k_parent 0.00735 7.64e-21 0.00641 0.00843 -## sigma 7.94557 1.83e-15 6.46713 9.42401 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 -## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03 -## N_parent 2.45e+00 NA 1.35e+00 3.54e+00 -## sigma 7.42e+00 NA 6.04e+00 8.80e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 -## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 3.63e-10 5.00e-01 0.0000 Inf -## g 6.06e-01 2.19e-01 0.4826 0.7178 -## sigma 7.40e+00 2.97e-15 6.0201 8.7754 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 94.3 3.13e+02 9.43e+01 -## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 3.77e+09 1.91e+09 -## -## Representative half-life: -## [1] 454.55</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p7</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3661.661 3195.030 3174.145 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 3334.194</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.41796 4.80e-53 93.32245 99.51347</span></span> +<span><span class="co">## k_parent 0.00735 7.64e-21 0.00641 0.00843</span></span> +<span><span class="co">## sigma 7.94557 1.83e-15 6.46713 9.42401</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.92e+01 NA 9.55e+01 1.03e+02</span></span> +<span><span class="co">## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03</span></span> +<span><span class="co">## N_parent 2.45e+00 NA 1.35e+00 3.54e+00</span></span> +<span><span class="co">## sigma 7.42e+00 NA 6.04e+00 8.80e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 9.44e-49 95.4640 102.2573</span></span> +<span><span class="co">## k1 1.81e-02 1.75e-01 0.0116 0.0281</span></span> +<span><span class="co">## k2 3.63e-10 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 6.06e-01 2.19e-01 0.4826 0.7178</span></span> +<span><span class="co">## sigma 7.40e+00 2.97e-15 6.0201 8.7754</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 94.3 3.13e+02 9.43e+01</span></span> +<span><span class="co">## IORE 96.7 1.51e+03 4.55e+02</span></span> +<span><span class="co">## DFOP 96.4 3.77e+09 1.91e+09</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 454.55</span></span></code></pre> </div> </div> -<div id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50" class="anchor"></a>Examples where the representative half-life deviates from the observed DT50</h1> -<div id="example-on-page-8" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> +<div class="section level2"> +<h2 id="examples-where-the-representative-half-life-deviates-from-the-observed-dt50">Examples where the representative half-life deviates from the observed DT50<a class="anchor" aria-label="anchor" href="#examples-where-the-representative-half-life-deviates-from-the-observed-dt50"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-8">Example on page 8<a class="anchor" aria-label="anchor" href="#example-on-page-8"></a> +</h3> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p8</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p8"</span><span class="op">]</span><span class="op">]</span>, parms.ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k__iore_parent <span class="op">=</span> <span class="fl">1e-3</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 1996.9408 444.9237 547.5616 -## -## Critical sum of squares for checking the SFO model: -## [1] 477.4924 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.16549 6.53e-29 83.37344 92.95754 -## k_parent 0.00803 1.67e-13 0.00674 0.00957 -## sigma 7.44786 4.17e-10 5.66209 9.23363 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 -## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04 -## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00 -## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 95.70619 8.99e-32 91.87941 99.53298 -## k1 0.02500 5.25e-04 0.01422 0.04394 -## k2 0.00273 6.84e-03 0.00125 0.00597 -## g 0.58835 2.84e-06 0.36595 0.77970 -## sigma 3.90001 6.94e-10 2.96260 4.83741 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 86.3 287 86.3 -## IORE 53.4 668 201.0 -## DFOP 55.6 517 253.0 -## -## Representative half-life: -## [1] 201.03</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p8</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 1996.9408 444.9237 547.5616 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 477.4924</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.16549 6.53e-29 83.37344 92.95754</span></span> +<span><span class="co">## k_parent 0.00803 1.67e-13 0.00674 0.00957</span></span> +<span><span class="co">## sigma 7.44786 4.17e-10 5.66209 9.23363</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02</span></span> +<span><span class="co">## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04</span></span> +<span><span class="co">## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00</span></span> +<span><span class="co">## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.70619 8.99e-32 91.87941 99.53298</span></span> +<span><span class="co">## k1 0.02500 5.25e-04 0.01422 0.04394</span></span> +<span><span class="co">## k2 0.00273 6.84e-03 0.00125 0.00597</span></span> +<span><span class="co">## g 0.58835 2.84e-06 0.36595 0.77970</span></span> +<span><span class="co">## sigma 3.90001 6.94e-10 2.96260 4.83741</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 86.3 287 86.3</span></span> +<span><span class="co">## IORE 53.4 668 201.0</span></span> +<span><span class="co">## DFOP 55.6 517 253.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 201.03</span></span></code></pre> </div> </div> -<div id="examples-where-sfo-was-not-selected-for-an-abiotic-study" class="section level1"> -<h1 class="hasAnchor"> -<a href="#examples-where-sfo-was-not-selected-for-an-abiotic-study" class="anchor"></a>Examples where SFO was not selected for an abiotic study</h1> -<div id="example-on-page-9-upper-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> +<div class="section level2"> +<h2 id="examples-where-sfo-was-not-selected-for-an-abiotic-study">Examples where SFO was not selected for an abiotic study<a class="anchor" aria-label="anchor" href="#examples-where-sfo-was-not-selected-for-an-abiotic-study"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-9-upper-panel">Example on page 9, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-upper-panel"></a> +</h3> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p9a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> <div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 839.35238 88.57064 9.93363 -## -## Critical sum of squares for checking the SFO model: -## [1] 105.5678 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933 3.06e-12 79.9447 96.4419 -## k_parent 0.0409 2.07e-07 0.0324 0.0516 -## sigma 7.2429 3.92e-05 4.4768 10.0090 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 -## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04 -## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00 -## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.85e+01 2.54e-20 97.390 99.672 -## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 9.02e-13 5.00e-01 0.000 Inf -## g 6.52e-01 8.13e-06 0.642 0.661 -## sigma 7.88e-01 6.13e-02 0.481 1.095 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 16.9 5.63e+01 1.69e+01 -## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.38e+12 7.69e+11 -## -## Representative half-life: -## [1] 101.43</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 839.35238 88.57064 9.93363 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 105.5678</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.1933 3.06e-12 79.9447 96.4419</span></span> +<span><span class="co">## k_parent 0.0409 2.07e-07 0.0324 0.0516</span></span> +<span><span class="co">## sigma 7.2429 3.92e-05 4.4768 10.0090</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02</span></span> +<span><span class="co">## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04</span></span> +<span><span class="co">## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00</span></span> +<span><span class="co">## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 9.85e+01 2.54e-20 97.390 99.672</span></span> +<span><span class="co">## k1 1.38e-01 3.52e-05 0.131 0.146</span></span> +<span><span class="co">## k2 9.02e-13 5.00e-01 0.000 Inf</span></span> +<span><span class="co">## g 6.52e-01 8.13e-06 0.642 0.661</span></span> +<span><span class="co">## sigma 7.88e-01 6.13e-02 0.481 1.095</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 16.9 5.63e+01 1.69e+01</span></span> +<span><span class="co">## IORE 11.6 3.37e+02 1.01e+02</span></span> +<span><span class="co">## DFOP 10.5 1.38e+12 7.69e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 101.43</span></span></code></pre> <p>In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.</p> </div> -<div id="example-on-page-9-lower-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> +<div class="section level3"> +<h3 id="example-on-page-9-lower-panel">Example on page 9, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-9-lower-panel"></a> +</h3> <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p9b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p9b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb44"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> <div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 35.64867 23.22334 35.64867 -## -## Critical sum of squares for checking the SFO model: -## [1] 28.54188 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 2.15e-19 93.178 96.2464 -## k_parent 0.0389 4.47e-14 0.037 0.0408 -## sigma 1.5957 1.28e-04 0.932 2.2595 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 93.863 2.32e-18 92.4565 95.269 -## k__iore_parent 0.127 1.85e-02 0.0504 0.321 -## N_parent 0.711 1.88e-05 0.4843 0.937 -## sigma 1.288 1.76e-04 0.7456 1.830 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.7123 1.61e-16 93.1355 96.2891 -## k1 0.0389 1.08e-04 0.0266 0.0569 -## k2 0.0389 2.23e-04 0.0255 0.0592 -## g 0.5256 NaN NA NA -## sigma 1.5957 2.50e-04 0.9135 2.2779 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 17.8 59.2 17.8 -## IORE 18.4 49.2 14.8 -## DFOP 17.8 59.2 17.8 -## -## Representative half-life: -## [1] 14.8</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p9b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 35.64867 23.22334 35.64867 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 28.54188</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 2.15e-19 93.178 96.2464</span></span> +<span><span class="co">## k_parent 0.0389 4.47e-14 0.037 0.0408</span></span> +<span><span class="co">## sigma 1.5957 1.28e-04 0.932 2.2595</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 93.863 2.32e-18 92.4565 95.269</span></span> +<span><span class="co">## k__iore_parent 0.127 1.85e-02 0.0504 0.321</span></span> +<span><span class="co">## N_parent 0.711 1.88e-05 0.4843 0.937</span></span> +<span><span class="co">## sigma 1.288 1.76e-04 0.7456 1.830</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 94.7123 1.61e-16 93.1355 96.2891</span></span> +<span><span class="co">## k1 0.0389 1.08e-04 0.0266 0.0569</span></span> +<span><span class="co">## k2 0.0389 2.23e-04 0.0255 0.0592</span></span> +<span><span class="co">## g 0.5256 NaN NA NA</span></span> +<span><span class="co">## sigma 1.5957 2.50e-04 0.9135 2.2779</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 17.8 59.2 17.8</span></span> +<span><span class="co">## IORE 18.4 49.2 14.8</span></span> +<span><span class="co">## DFOP 17.8 59.2 17.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 14.8</span></span></code></pre> <p>Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.</p> </div> -<div id="example-on-page-10" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> +<div class="section level3"> +<h3 id="example-on-page-10">Example on page 10<a class="anchor" aria-label="anchor" href="#example-on-page-10"></a> +</h3> <div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p10</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p10"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb53"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> <div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 899.4089 336.4348 899.4089 -## -## Critical sum of squares for checking the SFO model: -## [1] 413.4841 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 6.42e-11 91.9259 111.5371 -## k_parent 0.0495 1.70e-07 0.0404 0.0607 -## sigma 8.0152 1.28e-04 4.6813 11.3491 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.86 3.32e-12 90.848 102.863 -## k__iore_parent 2.96 7.91e-02 0.687 12.761 -## N_parent 0.00 5.00e-01 -0.372 0.372 -## sigma 4.90 1.77e-04 2.837 6.968 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.7315 1.41e-09 91.6534 111.8097 -## k1 0.0495 6.58e-03 0.0303 0.0809 -## k2 0.0495 2.60e-03 0.0410 0.0598 -## g 0.4487 5.00e-01 NA NA -## sigma 8.0152 2.50e-04 4.5886 11.4418 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 14.0 46.5 14.00 -## IORE 16.4 29.4 8.86 -## DFOP 14.0 46.5 14.00 -## -## Representative half-life: -## [1] 8.86</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p10</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 899.4089 336.4348 899.4089 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 413.4841</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 6.42e-11 91.9259 111.5371</span></span> +<span><span class="co">## k_parent 0.0495 1.70e-07 0.0404 0.0607</span></span> +<span><span class="co">## sigma 8.0152 1.28e-04 4.6813 11.3491</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.86 3.32e-12 90.848 102.863</span></span> +<span><span class="co">## k__iore_parent 2.96 7.91e-02 0.687 12.761</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -0.372 0.372</span></span> +<span><span class="co">## sigma 4.90 1.77e-04 2.837 6.968</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 101.7315 1.41e-09 91.6534 111.8097</span></span> +<span><span class="co">## k1 0.0495 6.58e-03 0.0303 0.0809</span></span> +<span><span class="co">## k2 0.0495 2.60e-03 0.0410 0.0598</span></span> +<span><span class="co">## g 0.4487 5.00e-01 NA NA</span></span> +<span><span class="co">## sigma 8.0152 2.50e-04 4.5886 11.4418</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 14.0 46.5 14.00</span></span> +<span><span class="co">## IORE 16.4 29.4 8.86</span></span> +<span><span class="co">## DFOP 14.0 46.5 14.00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.86</span></span></code></pre> <p>Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.</p> </div> </div> -<div id="the-dt50-was-not-observed-during-the-study" class="section level1"> -<h1 class="hasAnchor"> -<a href="#the-dt50-was-not-observed-during-the-study" class="anchor"></a>The DT50 was not observed during the study</h1> -<div id="example-on-page-11" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> +<div class="section level2"> +<h2 id="the-dt50-was-not-observed-during-the-study">The DT50 was not observed during the study<a class="anchor" aria-label="anchor" href="#the-dt50-was-not-observed-during-the-study"></a> +</h2> +<div class="section level3"> +<h3 id="example-on-page-11">Example on page 11<a class="anchor" aria-label="anchor" href="#example-on-page-11"></a> +</h3> <div class="sourceCode" id="cb56"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p11</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p11"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> <div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 579.6805 204.7932 144.7783 -## -## Critical sum of squares for checking the SFO model: -## [1] 251.6944 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 -## k_parent 0.00321 4.71e-05 0.00222 4.64e-03 -## sigma 6.43473 1.28e-04 3.75822 9.11e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 -## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14 -## N_parent 8.36e+00 NA 6.62e+00 1.01e+01 -## sigma 3.82e+00 NA 2.21e+00 5.44e+00 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 -## k1 4.41e-02 5.95e-03 0.0296 0.0658 -## k2 9.94e-13 5.00e-01 0.0000 Inf -## g 3.22e-01 1.45e-03 0.2814 0.3650 -## sigma 3.22e+00 3.52e-04 1.8410 4.5906 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 2.16e+02 7.18e+02 2.16e+02 -## IORE 9.73e+02 1.37e+08 4.11e+07 -## DFOP 3.07e+11 1.93e+12 6.98e+11 -## -## Representative half-life: -## [1] 41148170</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p11</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 579.6805 204.7932 144.7783 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 251.6944</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.15820 4.83e-13 90.24934 1.02e+02</span></span> +<span><span class="co">## k_parent 0.00321 4.71e-05 0.00222 4.64e-03</span></span> +<span><span class="co">## sigma 6.43473 1.28e-04 3.75822 9.11e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 NA 9.90e+01 1.10e+02</span></span> +<span><span class="co">## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14</span></span> +<span><span class="co">## N_parent 8.36e+00 NA 6.62e+00 1.01e+01</span></span> +<span><span class="co">## sigma 3.82e+00 NA 2.21e+00 5.44e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.05e+02 9.47e-13 99.9990 109.1224</span></span> +<span><span class="co">## k1 4.41e-02 5.95e-03 0.0296 0.0658</span></span> +<span><span class="co">## k2 9.94e-13 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## g 3.22e-01 1.45e-03 0.2814 0.3650</span></span> +<span><span class="co">## sigma 3.22e+00 3.52e-04 1.8410 4.5906</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.16e+02 7.18e+02 2.16e+02</span></span> +<span><span class="co">## IORE 9.73e+02 1.37e+08 4.11e+07</span></span> +<span><span class="co">## DFOP 3.07e+11 1.93e+12 6.98e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41148170</span></span></code></pre> <p>In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.</p> </div> </div> -<div id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="section level1"> -<h1 class="hasAnchor"> -<a href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant" class="anchor"></a>N is less than 1 and the DFOP rate constants are like the SFO rate constant</h1> +<div class="section level2"> +<h2 id="n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant">N is less than 1 and the DFOP rate constants are like the SFO rate constant<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant"></a> +</h2> <p>In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.</p> -<div id="example-on-page-12-upper-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> +<div class="section level3"> +<h3 id="example-on-page-12-upper-panel">Example on page 12, upper panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-upper-panel"></a> +</h3> <div class="sourceCode" id="cb62"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance -## matrix</code></pre> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p12a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance</span></span> +<span><span class="co">## matrix</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> <div class="sourceCode" id="cb71"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 695.4440 220.0685 695.4440 -## -## Critical sum of squares for checking the SFO model: -## [1] 270.4679 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 8.75e-12 92.461 108.581 -## k_parent 0.124 3.61e-08 0.104 0.148 -## sigma 7.048 1.28e-04 4.116 9.980 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.823 NA NA NA -## k__iore_parent 2.436 NA NA NA -## N_parent 0.263 NA NA NA -## sigma 3.965 NA NA NA -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.521 2.74e-10 92.2366 108.805 -## k1 0.124 2.53e-05 0.0908 0.170 -## k2 0.124 2.52e-02 0.0456 0.339 -## g 0.793 NaN NA NA -## sigma 7.048 2.50e-04 4.0349 10.061 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 5.58 18.5 5.58 -## IORE 6.49 13.2 3.99 -## DFOP 5.58 18.5 5.58 -## -## Representative half-life: -## [1] 3.99</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 695.4440 220.0685 695.4440 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 270.4679</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 8.75e-12 92.461 108.581</span></span> +<span><span class="co">## k_parent 0.124 3.61e-08 0.104 0.148</span></span> +<span><span class="co">## sigma 7.048 1.28e-04 4.116 9.980</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 96.823 NA NA NA</span></span> +<span><span class="co">## k__iore_parent 2.436 NA NA NA</span></span> +<span><span class="co">## N_parent 0.263 NA NA NA</span></span> +<span><span class="co">## sigma 3.965 NA NA NA</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 100.521 2.74e-10 92.2366 108.805</span></span> +<span><span class="co">## k1 0.124 2.53e-05 0.0908 0.170</span></span> +<span><span class="co">## k2 0.124 2.52e-02 0.0456 0.339</span></span> +<span><span class="co">## g 0.793 NaN NA NA</span></span> +<span><span class="co">## sigma 7.048 2.50e-04 4.0349 10.061</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 5.58 18.5 5.58</span></span> +<span><span class="co">## IORE 6.49 13.2 3.99</span></span> +<span><span class="co">## DFOP 5.58 18.5 5.58</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 3.99</span></span></code></pre> </div> -<div id="example-on-page-12-lower-panel" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> +<div class="section level3"> +<h3 id="example-on-page-12-lower-panel">Example on page 12, lower panel<a class="anchor" aria-label="anchor" href="#example-on-page-12-lower-panel"></a> +</h3> <div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in qt(alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in qt(1 - alpha/2, rdf): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs produced</code></pre> -<pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p12b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p12b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in qt(alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in qt(1 - alpha/2, rdf): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar_notrans)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> <div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 58.90242 19.06353 58.90242 -## -## Critical sum of squares for checking the SFO model: -## [1] 51.51756 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 0.00039 85.9388 109.4292 -## k_parent 0.0589 0.00261 0.0431 0.0805 -## sigma 3.4323 0.04356 -1.2377 8.1023 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.523 0.0055 74.539157 116.51 -## k__iore_parent 0.333 0.1433 0.000717 154.57 -## N_parent 0.568 0.0677 -0.989464 2.13 -## sigma 1.953 0.0975 -5.893100 9.80 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840 NaN NaN NaN -## k1 0.0589 NaN NA NA -## k2 0.0589 NaN NA NA -## g 0.6473 NaN NA NA -## sigma 3.4323 NaN NaN NaN -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 11.8 39.1 11.80 -## IORE 12.9 31.4 9.46 -## DFOP 11.8 39.1 11.80 -## -## Representative half-life: -## [1] 9.46</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p12b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 58.90242 19.06353 58.90242 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 51.51756</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 0.00039 85.9388 109.4292</span></span> +<span><span class="co">## k_parent 0.0589 0.00261 0.0431 0.0805</span></span> +<span><span class="co">## sigma 3.4323 0.04356 -1.2377 8.1023</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.523 0.0055 74.539157 116.51</span></span> +<span><span class="co">## k__iore_parent 0.333 0.1433 0.000717 154.57</span></span> +<span><span class="co">## N_parent 0.568 0.0677 -0.989464 2.13</span></span> +<span><span class="co">## sigma 1.953 0.0975 -5.893100 9.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.6840 NaN NaN NaN</span></span> +<span><span class="co">## k1 0.0589 NaN NA NA</span></span> +<span><span class="co">## k2 0.0589 NaN NA NA</span></span> +<span><span class="co">## g 0.6473 NaN NA NA</span></span> +<span><span class="co">## sigma 3.4323 NaN NaN NaN</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 11.8 39.1 11.80</span></span> +<span><span class="co">## IORE 12.9 31.4 9.46</span></span> +<span><span class="co">## DFOP 11.8 39.1 11.80</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 9.46</span></span></code></pre> </div> -<div id="example-on-page-13" class="section level2"> -<h2 class="hasAnchor"> -<a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> +<div class="section level3"> +<h3 id="example-on-page-13">Example on page 13<a class="anchor" aria-label="anchor" href="#example-on-page-13"></a> +</h3> <div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p13</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p13"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb86"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> <div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 174.5971 142.3951 174.5971 -## -## Critical sum of squares for checking the SFO model: -## [1] 172.131 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 5.99e-17 89.61936 95.85065 -## k_parent 0.00258 2.42e-09 0.00223 0.00299 -## sigma 3.41172 7.07e-05 2.05455 4.76888 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.6016 6.34e-16 88.53086 94.672 -## k__iore_parent 0.0396 2.36e-01 0.00207 0.759 -## N_parent 0.3541 1.46e-01 -0.35153 1.060 -## sigma 3.0811 9.64e-05 1.84296 4.319 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.73500 NA 8.95e+01 95.92118 -## k1 0.00258 NA 4.14e-04 0.01611 -## k2 0.00258 NA 1.74e-03 0.00383 -## g 0.16452 NA 0.00e+00 1.00000 -## sigma 3.41172 NA 2.02e+00 4.79960 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 269 892 269 -## IORE 261 560 169 -## DFOP 269 892 269 -## -## Representative half-life: -## [1] 168.51</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p13</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 174.5971 142.3951 174.5971 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 172.131</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 5.99e-17 89.61936 95.85065</span></span> +<span><span class="co">## k_parent 0.00258 2.42e-09 0.00223 0.00299</span></span> +<span><span class="co">## sigma 3.41172 7.07e-05 2.05455 4.76888</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 91.6016 6.34e-16 88.53086 94.672</span></span> +<span><span class="co">## k__iore_parent 0.0396 2.36e-01 0.00207 0.759</span></span> +<span><span class="co">## N_parent 0.3541 1.46e-01 -0.35153 1.060</span></span> +<span><span class="co">## sigma 3.0811 9.64e-05 1.84296 4.319</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 92.73500 NA 8.95e+01 95.92118</span></span> +<span><span class="co">## k1 0.00258 NA 4.14e-04 0.01611</span></span> +<span><span class="co">## k2 0.00258 NA 1.74e-03 0.00383</span></span> +<span><span class="co">## g 0.16452 NA 0.00e+00 1.00000</span></span> +<span><span class="co">## sigma 3.41172 NA 2.02e+00 4.79960</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 269 892 269</span></span> +<span><span class="co">## IORE 261 560 169</span></span> +<span><span class="co">## DFOP 269 892 269</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 168.51</span></span></code></pre> </div> </div> -<div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> -<h1 class="hasAnchor"> -<a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> +<div class="section level2"> +<h2 id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf">DT50 not observed in the study and DFOP problems in PestDF<a class="anchor" aria-label="anchor" href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf"></a> +</h2> <div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p14</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p14"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb95"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> <div class="sourceCode" id="cb96"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 48.43249 28.67746 27.26248 -## -## Critical sum of squares for checking the SFO model: -## [1] 32.83337 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 -## k_parent 0.00279 3.75e-15 0.00256 3.04e-03 -## sigma 1.55616 3.81e-06 1.03704 2.08e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 NA NaN NaN -## k__iore_parent 9.44e-08 NA NaN NaN -## N_parent 3.31e+00 NA NaN NaN -## sigma 1.20e+00 NA 0.796 1.6 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 -## k1 9.53e-03 1.20e-01 0.00638 0.0143 -## k2 6.08e-12 5.00e-01 0.00000 Inf -## g 3.98e-01 2.19e-01 0.30481 0.4998 -## sigma 1.17e+00 7.68e-06 0.77406 1.5610 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 2.48e+02 8.25e+02 2.48e+02 -## IORE 4.34e+02 2.22e+04 6.70e+03 -## DFOP 3.05e+10 2.95e+11 1.14e+11 -## -## Representative half-life: -## [1] 6697.44</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p14</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 48.43249 28.67746 27.26248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 32.83337</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.47124 2.06e-30 98.42254 1.01e+02</span></span> +<span><span class="co">## k_parent 0.00279 3.75e-15 0.00256 3.04e-03</span></span> +<span><span class="co">## sigma 1.55616 3.81e-06 1.03704 2.08e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 NA NaN NaN</span></span> +<span><span class="co">## k__iore_parent 9.44e-08 NA NaN NaN</span></span> +<span><span class="co">## N_parent 3.31e+00 NA NaN NaN</span></span> +<span><span class="co">## sigma 1.20e+00 NA 0.796 1.6</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.00e+02 2.96e-28 99.40280 101.2768</span></span> +<span><span class="co">## k1 9.53e-03 1.20e-01 0.00638 0.0143</span></span> +<span><span class="co">## k2 6.08e-12 5.00e-01 0.00000 Inf</span></span> +<span><span class="co">## g 3.98e-01 2.19e-01 0.30481 0.4998</span></span> +<span><span class="co">## sigma 1.17e+00 7.68e-06 0.77406 1.5610</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 2.48e+02 8.25e+02 2.48e+02</span></span> +<span><span class="co">## IORE 4.34e+02 2.22e+04 6.70e+03</span></span> +<span><span class="co">## DFOP 3.05e+10 2.95e+11 1.14e+11</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 6697.44</span></span></code></pre> <p>The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.</p> </div> -<div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> -<h1 class="hasAnchor"> -<a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> +<div class="section level2"> +<h2 id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero">N is less than 1 and DFOP fraction parameter is below zero<a class="anchor" aria-label="anchor" href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero"></a> +</h2> <div class="sourceCode" id="cb98"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p15a</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15a"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb101"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> <div class="sourceCode" id="cb102"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 245.5248 135.0132 245.5248 -## -## Critical sum of squares for checking the SFO model: -## [1] 165.9335 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 2.00e-15 94.32049 101.615 -## k_parent 0.00952 4.93e-09 0.00824 0.011 -## sigma 4.18778 1.28e-04 2.44588 5.930 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.874 2.94e-15 92.937 98.811 -## k__iore_parent 0.629 2.11e-01 0.044 8.982 -## N_parent 0.000 5.00e-01 -0.642 0.642 -## sigma 3.105 1.78e-04 1.795 4.416 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.96751 2.85e-13 94.21913 101.7159 -## k1 0.00952 6.28e-02 0.00250 0.0363 -## k2 0.00952 1.27e-04 0.00646 0.0140 -## g 0.21241 5.00e-01 0.00000 1.0000 -## sigma 4.18778 2.50e-04 2.39747 5.9781 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 72.8 242 72.8 -## IORE 76.3 137 41.3 -## DFOP 72.8 242 72.8 -## -## Representative half-life: -## [1] 41.33</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15a</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 245.5248 135.0132 245.5248 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 165.9335</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.00e-15 94.32049 101.615</span></span> +<span><span class="co">## k_parent 0.00952 4.93e-09 0.00824 0.011</span></span> +<span><span class="co">## sigma 4.18778 1.28e-04 2.44588 5.930</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 95.874 2.94e-15 92.937 98.811</span></span> +<span><span class="co">## k__iore_parent 0.629 2.11e-01 0.044 8.982</span></span> +<span><span class="co">## N_parent 0.000 5.00e-01 -0.642 0.642</span></span> +<span><span class="co">## sigma 3.105 1.78e-04 1.795 4.416</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 97.96751 2.85e-13 94.21913 101.7159</span></span> +<span><span class="co">## k1 0.00952 6.28e-02 0.00250 0.0363</span></span> +<span><span class="co">## k2 0.00952 1.27e-04 0.00646 0.0140</span></span> +<span><span class="co">## g 0.21241 5.00e-01 0.00000 1.0000</span></span> +<span><span class="co">## sigma 4.18778 2.50e-04 2.39747 5.9781</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 72.8 242 72.8</span></span> +<span><span class="co">## IORE 76.3 137 41.3</span></span> +<span><span class="co">## DFOP 72.8 242 72.8</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 41.33</span></span></code></pre> <div class="sourceCode" id="cb104"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## Warning in sqrt(diag(covar)): NaNs produced</code></pre> -<pre><code>## Warning in sqrt(1/diag(V)): NaNs produced</code></pre> -<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is -## doubtful</code></pre> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The half-life obtained from the IORE model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p15b</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p15b"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> +<pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is</span></span> +<span><span class="co">## doubtful</span></span></code></pre> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The half-life obtained from the IORE model may be used</span></span></code></pre> <div class="sourceCode" id="cb110"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> <div class="sourceCode" id="cb111"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 106.91629 68.55574 106.91629 -## -## Critical sum of squares for checking the SFO model: -## [1] 84.25618 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 -## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03 -## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.83 1.81e-16 97.51349 102.14 -## k__iore_parent 0.38 3.22e-01 0.00352 41.05 -## N_parent 0.00 5.00e-01 -1.07696 1.08 -## sigma 2.21 2.57e-04 1.23245 3.19 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.01e+02 NA 9.82e+01 1.04e+02 -## k1 4.86e-03 NA 8.63e-04 2.73e-02 -## k2 4.86e-03 NA 3.21e-03 7.35e-03 -## g 1.88e-01 NA NA NA -## sigma 2.76e+00 NA 1.58e+00 3.94e+00 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 143 474 143.0 -## IORE 131 236 71.2 -## DFOP 143 474 143.0 -## -## Representative half-life: -## [1] 71.18</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p15b</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 106.91629 68.55574 106.91629 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 84.25618</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02</span></span> +<span><span class="co">## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03</span></span> +<span><span class="co">## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 99.83 1.81e-16 97.51349 102.14</span></span> +<span><span class="co">## k__iore_parent 0.38 3.22e-01 0.00352 41.05</span></span> +<span><span class="co">## N_parent 0.00 5.00e-01 -1.07696 1.08</span></span> +<span><span class="co">## sigma 2.21 2.57e-04 1.23245 3.19</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 1.01e+02 NA 9.82e+01 1.04e+02</span></span> +<span><span class="co">## k1 4.86e-03 NA 8.63e-04 2.73e-02</span></span> +<span><span class="co">## k2 4.86e-03 NA 3.21e-03 7.35e-03</span></span> +<span><span class="co">## g 1.88e-01 NA NA NA</span></span> +<span><span class="co">## sigma 2.76e+00 NA 1.58e+00 3.94e+00</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 143 474 143.0</span></span> +<span><span class="co">## IORE 131 236 71.2</span></span> +<span><span class="co">## DFOP 143 474 143.0</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 71.18</span></span></code></pre> <p>In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.</p> </div> -<div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> -<h1 class="hasAnchor"> -<a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> +<div class="section level2"> +<h2 id="the-dfop-fraction-parameter-is-greater-than-1">The DFOP fraction parameter is greater than 1<a class="anchor" aria-label="anchor" href="#the-dfop-fraction-parameter-is-greater-than-1"></a> +</h2> <div class="sourceCode" id="cb113"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></code></pre></div> -<pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> -<pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> -<pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> -<pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> +<code class="sourceCode R"><span><span class="va">p16</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p16"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life of the IORE model is longer than the one corresponding</span></span></code></pre> +<pre><code><span><span class="co">## to the terminal degradation rate found with the DFOP model.</span></span></code></pre> +<pre><code><span><span class="co">## The representative half-life obtained from the DFOP model may be used</span></span></code></pre> <div class="sourceCode" id="cb118"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> <div class="sourceCode" id="cb119"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></code></pre></div> -<pre><code>## Sums of squares: -## SFO IORE DFOP -## 3831.804 2062.008 1550.980 -## -## Critical sum of squares for checking the SFO model: -## [1] 2247.348 -## -## Parameters: -## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.953 2.33e-13 60.509 83.40 -## k_parent 0.159 4.86e-05 0.102 0.25 -## sigma 11.302 1.25e-08 8.308 14.30 -## -## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 -## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595 -## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046 -## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062 -## -## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.5333 7.40e-18 79.9836 97.083 -## k1 18.8461 5.00e-01 0.0000 Inf -## k2 0.0776 1.41e-05 0.0518 0.116 -## g 0.4733 1.41e-09 0.3674 0.582 -## sigma 7.1902 2.11e-08 5.2785 9.102 -## -## -## DTx values: -## DT50 DT90 DT50_rep -## SFO 4.35 14.4 4.35 -## IORE 1.48 32.1 9.67 -## DFOP 0.67 21.4 8.93 -## -## Representative half-life: -## [1] 8.93</code></pre> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">p16</span><span class="op">)</span></span></code></pre></div> +<pre><code><span><span class="co">## Sums of squares:</span></span> +<span><span class="co">## SFO IORE DFOP </span></span> +<span><span class="co">## 3831.804 2062.008 1550.980 </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Critical sum of squares for checking the SFO model:</span></span> +<span><span class="co">## [1] 2247.348</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Parameters:</span></span> +<span><span class="co">## $SFO</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 71.953 2.33e-13 60.509 83.40</span></span> +<span><span class="co">## k_parent 0.159 4.86e-05 0.102 0.25</span></span> +<span><span class="co">## sigma 11.302 1.25e-08 8.308 14.30</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $IORE</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972</span></span> +<span><span class="co">## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595</span></span> +<span><span class="co">## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046</span></span> +<span><span class="co">## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## $DFOP</span></span> +<span><span class="co">## Estimate Pr(>t) Lower Upper</span></span> +<span><span class="co">## parent_0 88.5333 7.40e-18 79.9836 97.083</span></span> +<span><span class="co">## k1 18.8461 5.00e-01 0.0000 Inf</span></span> +<span><span class="co">## k2 0.0776 1.41e-05 0.0518 0.116</span></span> +<span><span class="co">## g 0.4733 1.41e-09 0.3674 0.582</span></span> +<span><span class="co">## sigma 7.1902 2.11e-08 5.2785 9.102</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## </span></span> +<span><span class="co">## DTx values:</span></span> +<span><span class="co">## DT50 DT90 DT50_rep</span></span> +<span><span class="co">## SFO 4.35 14.4 4.35</span></span> +<span><span class="co">## IORE 1.48 32.1 9.67</span></span> +<span><span class="co">## DFOP 0.67 21.4 8.93</span></span> +<span><span class="co">## </span></span> +<span><span class="co">## Representative half-life:</span></span> +<span><span class="co">## [1] 8.93</span></span></code></pre> <p>In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower <span class="math inline">\(\chi^2\)</span> error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.</p> </div> -<div id="conclusions" class="section level1"> -<h1 class="hasAnchor"> -<a href="#conclusions" class="anchor"></a>Conclusions</h1> +<div class="section level2"> +<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> +</h2> <p>The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.</p> <p>Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.</p> </div> -<div id="references" class="section level1 unnumbered"> -<h1 class="hasAnchor"> -<a href="#references" class="anchor"></a>References</h1> +<div class="section level2"> +<h2 class="unnumbered" id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> +</h2> <div id="refs" class="references hanging-indent"> <div id="ref-usepa2015"> <p>US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”</p> @@ -1016,11 +1027,13 @@ <footer><div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <p></p> +<p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p> +<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer> @@ -1029,5 +1042,7 @@ + + </body> </html> diff --git 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b/docs/dev/articles/web_only/benchmarks.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -112,7 +112,7 @@ <h1 data-toc-skip>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-15)</h4> + <h4 data-toc-skip class="date">Last change 14 July 2022 (rebuilt 2022-11-24)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -351,8 +351,16 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">2.129</td> -<td align="right">3.784</td> +<td align="right">2.140</td> +<td align="right">3.774</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">2.187</td> +<td align="right">3.851</td> </tr> </tbody> </table> @@ -530,9 +538,18 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">1.559</td> -<td align="right">6.097</td> -<td align="right">2.841</td> +<td align="right">1.554</td> +<td align="right">6.193</td> +<td align="right">2.843</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">1.585</td> +<td align="right">6.335</td> +<td align="right">3.003</td> </tr> </tbody> </table> @@ -764,12 +781,24 @@ <td align="left">Ryzen 7 1700</td> <td align="left">4.2.2</td> <td align="left">1.2.0</td> -<td align="right">0.911</td> -<td align="right">1.328</td> -<td align="right">1.519</td> -<td align="right">2.986</td> -<td align="right">1.957</td> -<td align="right">2.769</td> +<td align="right">0.913</td> +<td align="right">1.345</td> +<td align="right">1.539</td> +<td align="right">3.011</td> +<td align="right">1.987</td> +<td align="right">2.802</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 7 1700</td> +<td align="left">4.2.2</td> +<td align="left">1.2.2</td> +<td align="right">0.935</td> +<td align="right">1.381</td> +<td align="right">1.551</td> +<td align="right">3.209</td> +<td align="right">1.976</td> +<td align="right">3.013</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index ade86bc5..e9d80420 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -78,7 +78,10 @@ <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -109,7 +112,7 @@ <h1 data-toc-skip>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2022-11-01</h4> + <h4 data-toc-skip class="date">2022-11-24</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -167,10 +170,10 @@ <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.186</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.656 0.308</span></span> -<span><span class="co">## 2 Eigenvalue based 1 2.102 0.391</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 38.968 7.248</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.221</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.561 0.345</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.932 0.427</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 33.629 7.432</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> <div class="section level2"> @@ -197,10 +200,10 @@ <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.452</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 29.431 13.303</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 29 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.2.0 on</p> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.482</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 27.865 13.431</span></span></code></pre> +<p>Here we get a performance benefit of a factor of 28 using the version of the differential equation model compiled from C code!</p> +<p>This vignette was built with mkin 1.2.2 on</p> <pre><code><span><span class="co">## R version 4.2.2 (2022-10-31)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> <span><span class="co">## Running under: Debian GNU/Linux 11 (bullseye)</span></span></code></pre> diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html index 60f1ab5a..ec7f54d8 100644 --- a/docs/dev/articles/web_only/dimethenamid_2018.html +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,19 +63,25 @@ <a href="../../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -106,7 +112,7 @@ <h1 data-toc-skip>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 1 July 2022, built on 16 Sep 2022</h4> + <h4 data-toc-skip class="date">Last change 1 July 2022, built on 24 Nov 2022</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -366,7 +372,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> <span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix_methods_defaults</span><span class="op">)</span></span></code></pre></div> <pre><code> is gq lin -668.27 718.36 666.49 </code></pre> +669.77 669.36 670.95 </code></pre> </div> </div> <div class="section level3"> @@ -437,7 +443,7 @@ DFOP tc more iterations 665.88 663.80</code></pre> </h2> <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.1 (2022-06-23) +<pre><code>R version 4.2.2 (2022-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 11 (bullseye) @@ -457,24 +463,24 @@ attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] nlme_3.1-158 mkin_1.1.2 knitr_1.39 +[1] saemix_3.2 npde_3.2 nlme_3.1-160 mkin_1.2.2 knitr_1.41 loaded via a namespace (and not attached): - [1] deSolve_1.33 zoo_1.8-10 tidyselect_1.1.2 xfun_0.31 - [5] bslib_0.4.0 purrr_0.3.4 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.4.1 generics_0.1.3 htmltools_0.5.3 yaml_2.3.5 -[13] utf8_1.2.2 rlang_1.0.4 pkgdown_2.0.6 saemix_3.1 -[17] jquerylib_0.1.4 pillar_1.8.0 glue_1.6.2 DBI_1.1.3 -[21] lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0 gtable_0.3.0 -[25] ragg_1.2.2 memoise_2.0.1 evaluate_0.15 npde_3.2 -[29] fastmap_1.1.0 lmtest_0.9-40 parallel_4.2.1 fansi_1.0.3 -[33] highr_0.9 KernSmooth_2.23-20 scales_1.2.0 cachem_1.0.6 -[37] desc_1.4.1 jsonlite_1.8.0 systemfonts_1.0.4 fs_1.5.2 -[41] textshaping_0.3.6 gridExtra_2.3 ggplot2_3.3.6 digest_0.6.29 -[45] stringi_1.7.8 dplyr_1.0.9 grid_4.2.1 rprojroot_2.0.3 -[49] cli_3.3.0 tools_4.2.1 magrittr_2.0.3 sass_0.4.2 -[53] tibble_3.1.8 pkgconfig_2.0.3 assertthat_0.2.1 rmarkdown_2.14.3 -[57] mclust_5.4.10 R6_2.5.1 compiler_4.2.1 </code></pre> + [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.35 + [5] bslib_0.4.1 purrr_0.3.5 lattice_0.20-45 colorspace_2.0-3 + [9] vctrs_0.5.1 generics_0.1.3 htmltools_0.5.3 yaml_2.3.6 +[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.6 jquerylib_0.1.4 +[17] pillar_1.8.1 glue_1.6.2 DBI_1.1.3 lifecycle_1.0.3 +[21] stringr_1.4.1 munsell_0.5.0 gtable_0.3.1 ragg_1.2.4 +[25] codetools_0.2-18 memoise_2.0.1 evaluate_0.18 fastmap_1.1.0 +[29] lmtest_0.9-40 parallel_4.2.2 fansi_1.0.3 highr_0.9 +[33] scales_1.2.1 cachem_1.0.6 desc_1.4.2 jsonlite_1.8.3 +[37] systemfonts_1.0.4 fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 +[41] ggplot2_3.4.0 digest_0.6.30 stringi_1.7.8 dplyr_1.0.10 +[45] grid_4.2.2 rprojroot_2.0.3 cli_3.4.1 tools_4.2.2 +[49] magrittr_2.0.3 sass_0.4.3 tibble_3.1.8 pkgconfig_2.0.3 +[53] assertthat_0.2.1 rmarkdown_2.18 R6_2.5.1 mclust_6.0.0 +[57] compiler_4.2.2 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 50a57d1b..fd05f340 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -78,7 +78,10 @@ <a href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul> </li> @@ -109,7 +112,7 @@ <h1 data-toc-skip>Short demo of the multistart method</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-01)</h4> + <h4 data-toc-skip class="date">Last change 26 September 2022 (rebuilt 2022-11-24)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> @@ -163,8 +166,8 @@ <pre><code><span><span class="co">## Data: 155 observations of 1 variable(s) grouped in 6 datasets</span></span> <span><span class="co">## </span></span> <span><span class="co">## npar AIC BIC Lik Chisq Df Pr(>Chisq)</span></span> -<span><span class="co">## best(f_saem_reduced_multi) 9 663.64 661.77 -322.82 </span></span> -<span><span class="co">## f_saem_full 10 668.27 666.19 -324.13 0 1 1</span></span></code></pre> +<span><span class="co">## best(f_saem_reduced_multi) 9 663.69 661.82 -322.85 </span></span> +<span><span class="co">## f_saem_full 10 669.77 667.69 -324.89 0 1 1</span></span></code></pre> <p>While AIC and BIC are lower for the reduced model, the likelihood ratio test does not indicate a significant difference between the fits.</p> </div> diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png Binary files differindex 79543765..13bdb94b 100644 --- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png +++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-3-1.png diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png Binary files differindex 4466d437..56147ae2 100644 --- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png +++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-4-1.png diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png Binary files differindex 3dd36f91..f0b89dba 100644 --- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png +++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-5-1.png diff --git a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png Binary files differindex 3963e993..c57c247f 100644 --- a/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png +++ b/docs/dev/articles/web_only/multistart_files/figure-html/unnamed-chunk-6-1.png diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index afff038f..66f4b075 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -112,7 +112,7 @@ <h1 data-toc-skip>Benchmark timings for saem.mmkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-16)</h4> + <h4 data-toc-skip class="date">Last change 14 November 2022 (rebuilt 2022-11-24)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> <div class="hidden name"><code>saem_benchmarks.rmd</code></div> @@ -304,16 +304,28 @@ <th align="right">t3</th> <th align="right">t4</th> </tr></thead> -<tbody><tr class="odd"> +<tbody> +<tr class="odd"> <td align="left">Ryzen 7 1700</td> <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">2.156</td> -<td align="right">4.647</td> -<td align="right">4.296</td> -<td align="right">4.951</td> -</tr></tbody> +<td align="right">2.140</td> +<td align="right">4.626</td> +<td align="right">4.328</td> +<td align="right">4.998</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">2.427</td> +<td align="right">4.550</td> +<td align="right">4.217</td> +<td align="right">4.851</td> +</tr> +</tbody> </table> <p>Two-component error fits for SFO, DFOP, SFORB and HS.</p> <table class="table"> @@ -327,16 +339,28 @@ <th align="right">t7</th> <th align="right">t8</th> </tr></thead> -<tbody><tr class="odd"> +<tbody> +<tr class="odd"> <td align="left">Ryzen 7 1700</td> <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">5.645</td> -<td align="right">7.415</td> -<td align="right">7.848</td> -<td align="right">7.967</td> -</tr></tbody> +<td align="right">5.678</td> +<td align="right">7.441</td> +<td align="right">8.000</td> +<td align="right">7.980</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">5.352</td> +<td align="right">7.201</td> +<td align="right">8.174</td> +<td align="right">8.401</td> +</tr> +</tbody> </table> </div> <div class="section level3"> @@ -352,14 +376,24 @@ <th align="right">t9</th> <th align="right">t10</th> </tr></thead> -<tbody><tr class="odd"> +<tbody> +<tr class="odd"> <td align="left">Ryzen 7 1700</td> <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">24.182</td> -<td align="right">783.932</td> -</tr></tbody> +<td align="right">24.465</td> +<td align="right">800.266</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">25.193</td> +<td align="right">798.580</td> +</tr> +</tbody> </table> </div> <div class="section level3"> @@ -374,13 +408,22 @@ <th align="left">saemix</th> <th align="right">t11</th> </tr></thead> -<tbody><tr class="odd"> +<tbody> +<tr class="odd"> <td align="left">Ryzen 7 1700</td> <td align="left">Linux</td> <td align="left">1.2.0</td> <td align="left">3.2</td> -<td align="right">1322.5</td> -</tr></tbody> +<td align="right">1289.198</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 7 1700</td> +<td align="left">Linux</td> +<td align="left">1.2.2</td> +<td align="left">3.2</td> +<td align="right">1312.445</td> +</tr> +</tbody> </table> </div> </div> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 2f95f092..bd58bc3d 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -115,13 +115,13 @@ <p>Ranke J (2022). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.2.0, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.2, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2022}, - note = {R package version 1.2.0}, + note = {R package version 1.2.2}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/dev/index.html b/docs/dev/index.html index 4709fe29..2615d389 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -153,9 +153,9 @@ <h3 id="general">General<a class="anchor" aria-label="anchor" href="#general"></a> </h3> <ul> -<li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> -<li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> -<li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> +<li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two state variables for the observed variable.</li> +<li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation or some simple models involving a single transformation product, , an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> +<li>The usual one-sided t-test for significant difference from zero is shown based on estimators for the untransformed parameters.</li> <li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> <li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> <li>The ‘variance by variable’ error model which is often fitted using Iteratively Reweighted Least Squares (IRLS) can be specified as <code>error_model = "obs"</code>.</li> @@ -169,8 +169,8 @@ <li>Model comparisons using the Akaike Information Criterion (AIC) are supported which can also be used for non-constant variance. In such cases the FOCUS chi-squared error level is not meaningful.</li> <li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution.</li> <li>When parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which cannot occur in a single experiment with a single defined radiolabel position.</li> -<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model used by other tools for biphasic metabolite curves. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.</li> -<li>Nonlinear mixed-effects models can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> and <a href="https://pkgdown.jrwb.de/mkin/reference/saem.html">saem.mmkin</a> and methods. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils). The saem method uses the <code>saemix</code> package as a backend. Analytical solutions suitable for use with this package have been implemented for parent only models and the most important models including one metabolite (SFO-SFO and DFOP-SFO). Fitting other models with <code>saem.mmkin</code>, while it makes use of the compiled ODE models that mkin provides, has longer run times (at least six minutes on my system).</li> +<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite. Mathematically, the SFORB model is equivalent to the DFOP model. However, the SFORB model has the advantage that there is a mechanistic interpretation of the model parameters.</li> +<li>Nonlinear mixed-effects models (hierarchical models) can be created from fits of the same degradation model to different datasets for the same compound by using the <a href="https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html">nlme.mmkin</a> and <a href="https://pkgdown.jrwb.de/mkin/reference/saem.html">saem.mmkin</a> methods. Note that the convergence of the nlme fits depends on the quality of the data. Convergence is better for simple models and data for many groups (e.g. soils). The saem method uses the <code>saemix</code> package as a backend. Analytical solutions suitable for use with this package have been implemented for parent only models and the most important models including one metabolite (SFO-SFO and DFOP-SFO). Fitting other models with <code>saem.mmkin</code>, while it makes use of the compiled ODE models that mkin provides, has longer run times (from a couple of minutes to more than an hour).</li> </ul> </div> <div class="section level3"> @@ -186,7 +186,7 @@ <div class="section level2"> <h2 id="gui">GUI<a class="anchor" aria-label="anchor" href="#gui"></a> </h2> -<p>There is a graphical user interface that may be useful. Please refer to its <a href="https://pkgdown.jrwb.de/gmkin/" class="external-link">documentation page</a> for installation instructions and a manual.</p> +<p>There is a graphical user interface that may be useful. Please refer to its <a href="https://pkgdown.jrwb.de/gmkin/" class="external-link">documentation page</a> for installation instructions and a manual. It only supports evaluations using (generalised) nonlinear regression, but not simultaneous fits using nonlinear mixed-effects models.</p> </div> <div class="section level2"> <h2 id="news">News<a class="anchor" aria-label="anchor" href="#news"></a> @@ -203,8 +203,8 @@ <p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8" class="external-link">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin/" class="external-link">first CRAN version</a> on 18 May 2010.</p> <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, among other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="https://cake-kinetics.org" class="external-link">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> -<p>Finally, there is <a href="https://github.com/zhenglei-gao/KineticEval" class="external-link">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> -<p>Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.</p> +<p>Finally, there is <a href="https://github.com/zhenglei-gao/KineticEval" class="external-link">KineticEval</a>, which contains some further development of the scripts used for KinGUII.</p> +<p>Thanks to René Lehmann, formerly working at the Umweltbundesamt, for the nice cooperation on parameter transformations, especially the isometric log-ratio transformation that is now used for formation fractions in case there are more than two transformation targets.</p> <p>Many inspirations for improvements of mkin resulted from doing kinetic evaluations of degradation data for my clients while working at Harlan Laboratories and at Eurofins Regulatory AG, and now as an independent consultant.</p> <p>Funding was received from the Umweltbundesamt in the course of the projects</p> <ul> @@ -215,7 +215,8 @@ <li>Project Number 120667 (Development of objective criteria for the evaluation of the visual fit in the kinetic evaluation of degradation data, 2019-2020)</li> <li>Project Number 146839 (Checking the feasibility of using mixed-effects models for the derivation of kinetic modelling parameters from degradation studies, 2020-2021)</li> </ul> -<p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for the nice collaboration on using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p> +<p>Thanks to everyone involved for collaboration and support!</p> +<p>Thanks are due also to Emmanuelle Comets, maintainer of the saemix package, for her interest and support for using the SAEM algorithm and its implementation in saemix for the evaluation of chemical degradation data.</p> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 3353922b..50afb3e9 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -88,7 +88,19 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-unreleased">mkin 1.2.0 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-120-unreleased"></a></h2> +<h2 class="page-header" data-toc-text="1.2.2" id="mkin-122">mkin 1.2.2<a class="anchor" aria-label="anchor" href="#mkin-122"></a></h2> +<ul><li></ul></div> + <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2> +<ul><li><p>‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.</p></li> +<li><p>‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm</p></li> +<li><p>‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests</p></li> +<li><p>‘R/saem.R’: Fix a bug that prevented that ‘error.ini’ is passed to ‘saemix_model’, and set default to c(1, 1) to avoid changing test results</p></li> +<li><p>‘R/parplot.R’: Show initial values for error model parameters</p></li> +<li><p>‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel</p></li> +</ul></div> + <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> <ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> <li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> <li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 44bd60f5..0669ac9c 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -13,7 +13,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2022-11-16T14:17Z +last_built: 2022-11-24T06:50Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: 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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ same dataset." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the AIC for a column of an mmkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/AIC.mmkin.R" class="external-link"><code>R/AIC.mmkin.R</code></a></small> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -149,102 +94,110 @@ same dataset." /> same dataset.</p> </div> - <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, k <span class='op'>=</span> <span class='fl'>2</span><span class='op'>)</span> - -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, containing only one -column.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - <tr> - <th>k</th> - <td><p>As in the generic method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>As in the generic method (a numeric value for single fits, or a -dataframe if there are several fits in the column).</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one +column.</p></dd> + +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> + + +<dt>k</dt> +<dd><p>As in the generic method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>As in the generic method (a numeric value for single fits, or a +dataframe if there are several fits in the column).</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># skip, as it takes > 10 s on winbuilder</span> - <span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS A"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, - <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='co'># We get a warning because the FOMC model does not converge for the</span> - <span class='co'># FOCUS A dataset, as it is well described by SFO</span> - - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># We get a single number for a single fit</span> -</div><div class='output co'>#> [1] 55.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># or when extracting an mkinfit object</span> -</div><div class='output co'>#> [1] 55.28197</div><div class='input'> - <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span> - <span class='co'># of parameters, the higher (worse) the AIC</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> SFO 3 55.28197 -#> FOMC 4 57.28222 -#> DFOP 5 59.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span>, k <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># If we do not penalize additional parameters, we get nearly the same</span> -</div><div class='output co'>#> df AIC -#> SFO 3 49.28197 -#> FOMC 4 49.28222 -#> DFOP 5 49.28197</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS A"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Comparing the BIC gives a very similar picture</span> -</div><div class='output co'>#> df BIC -#> SFO 3 55.52030 -#> FOMC 4 57.59999 -#> DFOP 5 59.67918</div><div class='input'> - <span class='co'># For FOCUS C, the more complex models fit better</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> SFO 3 59.29336 -#> FOMC 4 44.68652 -#> DFOP 5 29.02372</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> df BIC -#> SFO 3 59.88504 -#> FOMC 4 45.47542 -#> DFOP 5 30.00984</div><div class='input'> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># skip, as it takes > 10 s on winbuilder</span></span></span> +<span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS A"</span> <span class="op">=</span> <span class="va">FOCUS_2006_A</span>,</span></span> +<span class="r-in"><span> <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="co"># We get a warning because the FOMC model does not converge for the</span></span></span> +<span class="r-in"><span> <span class="co"># FOCUS A dataset, as it is well described by SFO</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># We get a single number for a single fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span> <span class="co"># or when extracting an mkinfit object</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 55.28197</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS A, the models fit almost equally well, so the higher the number</span></span></span> +<span class="r-in"><span> <span class="co"># of parameters, the higher (worse) the AIC</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.28197</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.28222</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span>, k <span class="op">=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># If we do not penalize additional parameters, we get nearly the same</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 49.28197</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 49.28222</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 49.28197</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS A"</span><span class="op">]</span><span class="op">)</span> <span class="co"># Comparing the BIC gives a very similar picture</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df BIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 55.52030</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 57.59999</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 59.67918</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># For FOCUS C, the more complex models fit better</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.29336</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 44.68652</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 29.02372</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df BIC</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 3 59.88504</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC 4 45.47542</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 5 30.00984</span> +<span class="r-in"><span> </span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html index 47efd056..33ae3f74 100644 --- a/docs/dev/reference/CAKE_export.html +++ b/docs/dev/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><meta name="robots" content="noindex"><!-- mathjax --><scrip </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -45,19 +45,25 @@ specified as well."><meta name="robots" content="noindex"><!-- mathjax --><scrip <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index 5cf7604c..14840260 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><meta name="robots" content="noinde <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html index f41d8e9b..c6746fe7 100644 --- a/docs/dev/reference/DFOP.solution.html +++ b/docs/dev/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><meta name="robots" content="noindex"><!-- m </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ two exponential decline functions."><meta name="robots" content="noindex"><!-- m <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html index 8381337a..cd863616 100644 --- a/docs/dev/reference/Extract.mmkin.html +++ b/docs/dev/reference/Extract.mmkin.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Subsetting method for mmkin objects — [.mmkin • mkin</title> - - -<!-- jquery --> -<script 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--><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Subsetting method for mmkin objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>Extract.mmkin.Rd</code></div> </div> @@ -147,122 +92,127 @@ <p>Subsetting method for mmkin objects</p> </div> - <pre class="usage"># S3 method for mmkin -[(x, i, j, ..., drop = FALSE)</pre> + <div id="ref-usage"> + <div class="sourceCode"><pre><code># S3 method for mmkin +[(x, i, j, ..., drop = FALSE)</code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An <code><a href='mmkin.html'>mmkin</a> object</code></p></td> - </tr> - <tr> - <th>i</th> - <td><p>Row index selecting the fits for specific models</p></td> - </tr> - <tr> - <th>j</th> - <td><p>Column index selecting the fits to specific datasets</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used, only there to satisfy the generic method definition</p></td> - </tr> - <tr> - <th>drop</th> - <td><p>If FALSE, the method always returns an mmkin object, otherwise -either a list of mkinfit objects or a single mkinfit object.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>i</dt> +<dd><p>Row index selecting the fits for specific models</p></dd> - <p>An object of class <code><a href='mmkin.html'>mmkin</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +<dt>j</dt> +<dd><p>Column index selecting the fits to specific datasets</p></dd> + + +<dt>...</dt> +<dd><p>Not used, only there to satisfy the generic method definition</p></dd> + + +<dt>drop</dt> +<dd><p>If FALSE, the method always returns an mmkin object, otherwise +either a list of mkinfit objects or a single mkinfit object.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># Only use one core, to pass R CMD check --as-cran</span> - <span class='va'>fits</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span><span class='op'>)</span>, <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, - cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B C -#> FOMC OK OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> FOMC OK -#> -#> OK: No warnings</div><div class='input'> <span class='va'>fits</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span><span class='op'>]</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model B -#> SFO OK -#> -#> OK: No warnings</div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span><span class='op'>(</span> - <span class='co'># This extracts an mkinfit object with lots of components</span> - <span class='va'>fits</span><span class='op'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span><span class='op'>]</span><span class='op'>]</span> - <span class='op'>)</span> -</div><div class='output co'>#> $par -#> parent_0 log_alpha log_beta sigma -#> 99.666192 2.549850 5.050586 1.890202 -#> -#> $objective -#> [1] 28.58291 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 21 -#> -#> $evaluations -#> function gradient -#> 25 78 -#> -#> $message -#> [1] "both X-convergence and relative convergence (5)" -#> </div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B C </span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span>, <span class="st">"B"</span><span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="st">"B"</span><span class="op">]</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> <mmkin> object</span> +<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> dataset</span> +<span class="r-out co"><span class="r-pr">#></span> model B </span> +<span class="r-out co"><span class="r-pr">#></span> SFO OK</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="co"># This extracts an mkinfit object with lots of components</span></span></span> +<span class="r-in"><span> <span class="va">fits</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"B"</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $par</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_alpha log_beta sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 99.666192 2.549850 5.050586 1.890202 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $objective</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 28.58291</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $convergence</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $iterations</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 21</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $evaluations</span> +<span class="r-out co"><span class="r-pr">#></span> function gradient </span> +<span class="r-out co"><span class="r-pr">#></span> 25 78 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $message</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "both X-convergence and relative convergence (5)"</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html index a188430d..8891567a 100644 --- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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table with the fitted parameters and the resulting DT50 and DT90 values +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> @@ -155,59 +100,73 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>f</code></dt><dd><p>The fitted f parameter</p></dd> - <dt><code>k1</code></dt><dd><p>The fitted k1 parameter</p></dd> - <dt><code>k2</code></dt><dd><p>The fitted k2 parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>f</code></dt> +<dd><p>The fitted f parameter</p></dd> + + <dt><code>k1</code></dt> +<dd><p>The fitted k1 parameter</p></dd> + + <dt><code>k2</code></dt> +<dd><p>The fitted k2 parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_DFOP_ref_A_to_B</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 0bee1c16..a725ada7 100644 --- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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-<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> -<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F"><meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> @@ -155,58 +100,70 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>alpha</code></dt><dd><p>The fitted alpha parameter</p></dd> - <dt><code>beta</code></dt><dd><p>The fitted beta parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>alpha</code></dt> +<dd><p>The fitted alpha parameter</p></dd> + + <dt><code>beta</code></dt> +<dd><p>The fitted beta parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_FOMC_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</h1> @@ -155,59 +100,73 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_HS_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_HS_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>tb</code></dt><dd><p>The fitted tb parameter</p></dd> - <dt><code>k1</code></dt><dd><p>The fitted k1 parameter</p></dd> - <dt><code>k2</code></dt><dd><p>The fitted k2 parameter</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>tb</code></dt> +<dd><p>The fitted tb parameter</p></dd> + + <dt><code>k1</code></dt> +<dd><p>The fitted k1 parameter</p></dd> + + <dt><code>k2</code></dt> +<dd><p>The fitted k2 parameter</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_HS_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_HS_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html index c1a5fdff..445ed2d6 100644 --- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 -in this fit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ in this fit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,44 +45,46 @@ in this fit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</h1> @@ -155,57 +100,67 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> +<dd><p>a factor giving the name of the software package</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>M0</code></dt> +<dd><p>The fitted initial concentration of the parent compound</p></dd> - <p>A data frame containing the following variables.</p><dl> - <dt><code>package</code></dt><dd><p>a factor giving the name of the software package</p></dd> - <dt><code>M0</code></dt><dd><p>The fitted initial concentration of the parent compound</p></dd> - <dt><code>k</code></dt><dd><p>The fitted first-order degradation rate constant</p></dd> - <dt><code>DT50</code></dt><dd><p>The resulting half-life of the parent compound</p></dd> - <dt><code>DT90</code></dt><dd><p>The resulting DT90 of the parent compound</p></dd> - <dt><code>dataset</code></dt><dd><p>The FOCUS dataset that was used</p></dd> - -</dl> + <dt><code>k</code></dt> +<dd><p>The fitted first-order degradation rate constant</p></dd> + + <dt><code>DT50</code></dt> +<dd><p>The resulting half-life of the parent compound</p></dd> + + <dt><code>DT90</code></dt> +<dd><p>The resulting DT90 of the parent compound</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>dataset</code></dt> +<dd><p>The FOCUS dataset that was used</p></dd> - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_SFO_ref_A_to_F</span><span class='op'>)</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span><span class="op">)</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,44 +41,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets A to F from the FOCUS Kinetics report from 2006</h1> @@ -147,68 +92,73 @@ <p>Data taken from FOCUS (2006), p. 258.</p> </div> - <pre class="usage"><span class='va'>FOCUS_2006_A</span> - <span class='va'>FOCUS_2006_B</span> - <span class='va'>FOCUS_2006_C</span> - <span class='va'>FOCUS_2006_D</span> - <span class='va'>FOCUS_2006_E</span> - <span class='va'>FOCUS_2006_F</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_A</span></span> +<span> <span class="va">FOCUS_2006_B</span></span> +<span> <span class="va">FOCUS_2006_C</span></span> +<span> <span class="va">FOCUS_2006_D</span></span> +<span> <span class="va">FOCUS_2006_E</span></span> +<span> <span class="va">FOCUS_2006_F</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>6 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>a factor containing the name of the observed variable</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>time</code></dt> +<dd><p>a numeric vector containing time points</p></dd> - <p>6 datasets with observations on the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - -</dl> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + +</dl></div> + <div id="source"> + <h2>Source</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>FOCUS_2006_C</span> -</div><div class='output co'>#> name time value -#> 1 parent 0 85.1 -#> 2 parent 1 57.9 -#> 3 parent 3 29.9 -#> 4 parent 7 14.6 -#> 5 parent 14 9.7 -#> 6 parent 28 6.6 -#> 7 parent 63 4.0 -#> 8 parent 91 3.9 -#> 9 parent 119 0.6</div></pre> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_2006_C</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> name time value</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 0 85.1</span> +<span class="r-out co"><span class="r-pr">#></span> 2 parent 1 57.9</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 3 29.9</span> +<span class="r-out co"><span class="r-pr">#></span> 4 parent 7 14.6</span> +<span class="r-out co"><span class="r-pr">#></span> 5 parent 14 9.7</span> +<span class="r-out co"><span class="r-pr">#></span> 6 parent 28 6.6</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 63 4.0</span> +<span class="r-out co"><span class="r-pr">#></span> 8 parent 91 3.9</span> +<span class="r-out co"><span class="r-pr">#></span> 9 parent 119 0.6</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html index f64e759c..e1f19dc1 100644 --- a/docs/dev/reference/FOMC.solution.html +++ b/docs/dev/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><meta name="robots" content="noindex"><!-- mathjax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ a decreasing rate constant."><meta name="robots" content="noindex"><!-- mathjax <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html index 5fcef9c0..241d8d69 100644 --- a/docs/dev/reference/HS.solution.html +++ b/docs/dev/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><meta name="robots" content="noindex"><!-- mathjax --><script src </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ between them."><meta name="robots" content="noindex"><!-- mathjax --><script src <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html index 90eccde9..991fb566 100644 --- a/docs/dev/reference/IORE.solution.html +++ b/docs/dev/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><meta name="robots" content="noindex"> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - 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<a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Example datasets from the NAFTA SOP published 2015</h1> @@ -147,97 +92,107 @@ <p>Data taken from US EPA (2015), p. 19 and 23.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Appendix_B</span> - <span class='va'>NAFTA_SOP_Appendix_D</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Appendix_B</span></span> +<span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>2 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>a factor containing the name of the observed variable</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>time</code></dt> +<dd><p>a numeric vector containing time points</p></dd> - <p>2 datasets with observations on the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd> - -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 -#> -#> Representative half-life: -#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> +<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span> +<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="NAFTA_SOP_2015-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" 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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,44 +41,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1> @@ -147,91 +92,96 @@ <p>Data taken from from Attachment 1 of the SOP.</p> </div> - <pre class="usage"><span class='va'>NAFTA_SOP_Attachment</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Attachment</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable - for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + for the evaluation with <code><a href="nafta.html">nafta</a></code></p> + </div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>nafta_att_p5a</span> <span class='op'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span><span class='op'>(</span><span class='va'>NAFTA_SOP_Attachment</span><span class='op'>[[</span><span class='st'>"p5a"</span><span class='op'>]</span><span class='op'>]</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 465.21753 56.27506 32.06401 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 64.4304 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 95.8401 4.67e-21 92.245 99.4357 -#> k_parent 0.0102 3.92e-12 0.009 0.0117 -#> sigma 4.8230 3.81e-06 3.214 6.4318 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 1.01e+02 NA 9.91e+01 1.02e+02 -#> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 -#> N_parent 2.57e+00 NA 2.25e+00 2.89e+00 -#> sigma 1.68e+00 NA 1.12e+00 2.24e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 -#> k1 2.67e-02 5.05e-06 0.0243 0.0295 -#> k2 2.26e-12 5.00e-01 0.0000 Inf -#> g 6.47e-01 3.67e-06 0.6248 0.6677 -#> sigma 1.27e+00 8.91e-06 0.8395 1.6929 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 67.7 2.25e+02 6.77e+01 -#> IORE 58.2 1.07e+03 3.22e+02 -#> DFOP 55.5 5.59e+11 3.07e+11 -#> -#> Representative half-life: -#> [1] 321.51</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_att_p5a</span><span class='op'>)</span> -</div><div class='img'><img src='NAFTA_SOP_Attachment-1.png' alt='' width='700' height='433' /></div></pre> + <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The half-life obtained from the IORE model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 465.21753 56.27506 32.06401 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 64.4304</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 95.8401 4.67e-21 92.245 99.4357</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0102 3.92e-12 0.009 0.0117</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.8230 3.81e-06 3.214 6.4318</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.01e+02 NA 9.91e+01 1.02e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 2.57e+00 NA 2.25e+00 2.89e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.68e+00 NA 1.12e+00 2.24e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.99e+01 1.41e-26 98.8116 101.0810</span> +<span class="r-out co"><span class="r-pr">#></span> k1 2.67e-02 5.05e-06 0.0243 0.0295</span> +<span class="r-out co"><span class="r-pr">#></span> k2 2.26e-12 5.00e-01 0.0000 Inf</span> +<span class="r-out co"><span class="r-pr">#></span> g 6.47e-01 3.67e-06 0.6248 0.6677</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.27e+00 8.91e-06 0.8395 1.6929</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 67.7 2.25e+02 6.77e+01</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 58.2 1.07e+03 3.22e+02</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 55.5 5.59e+11 3.07e+11</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 321.51</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_att_p5a</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="NAFTA_SOP_Attachment-1.png" alt="" width="700" height="433"></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex b3448db0..ca982688 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 27feab09..de2d61aa 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot005.png b/docs/dev/reference/Rplot005.png Binary files differindex cb419daa..76f25647 100644 --- a/docs/dev/reference/Rplot005.png +++ b/docs/dev/reference/Rplot005.png diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html index 970a62c5..a0bb999c 100644 --- a/docs/dev/reference/SFO.solution.html +++ b/docs/dev/reference/SFO.solution.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html index e3e43557..c14d3a32 100644 --- a/docs/dev/reference/SFORB.solution.html +++ b/docs/dev/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ and no substance in the bound fraction."><meta name="robots" content="noindex">< <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/add_err-1.png b/docs/dev/reference/add_err-1.png Binary files differindex 9ba106db..4a3b4062 100644 --- a/docs/dev/reference/add_err-1.png +++ b/docs/dev/reference/add_err-1.png diff --git a/docs/dev/reference/add_err-2.png b/docs/dev/reference/add_err-2.png Binary files differindex 3088c40e..5aec1744 100644 --- a/docs/dev/reference/add_err-2.png +++ b/docs/dev/reference/add_err-2.png diff --git a/docs/dev/reference/add_err-3.png b/docs/dev/reference/add_err-3.png Binary files differindex 493a761a..2e71f02f 100644 --- a/docs/dev/reference/add_err-3.png +++ b/docs/dev/reference/add_err-3.png diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index b94cef29..c70d43a0 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> 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The variance of the error -may depend on the predicted value and is specified as a standard deviation." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +may depend on the predicted value and is specified as a standard deviation."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ may depend on the predicted value and is specified as a standard deviation." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,195 +43,203 @@ may depend on the predicted value and is specified as a standard deviation." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Add normally distributed errors to simulated kinetic degradation data</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/add_err.R'><code>R/add_err.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small> <div class="hidden name"><code>add_err.Rd</code></div> </div> <div class="ref-description"> <p>Normally distributed errors are added to data predicted for a specific -degradation model using <code><a href='mkinpredict.html'>mkinpredict</a></code>. The variance of the error +degradation model using <code><a href="mkinpredict.html">mkinpredict</a></code>. The variance of the error may depend on the predicted value and is specified as a standard deviation.</p> </div> - <pre class="usage"><span class='fu'>add_err</span><span class='op'>(</span> - <span class='va'>prediction</span>, - <span class='va'>sdfunc</span>, - secondary <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - n <span class='op'>=</span> <span class='fl'>10</span>, - LOD <span class='op'>=</span> <span class='fl'>0.1</span>, - reps <span class='op'>=</span> <span class='fl'>2</span>, - digits <span class='op'>=</span> <span class='fl'>1</span>, - seed <span class='op'>=</span> <span class='cn'>NA</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>prediction</th> - <td><p>A prediction from a kinetic model as produced by -<code><a href='mkinpredict.html'>mkinpredict</a></code>.</p></td> - </tr> - <tr> - <th>sdfunc</th> - <td><p>A function taking the predicted value as its only argument and + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span> +<span> <span class="va">prediction</span>,</span> +<span> <span class="va">sdfunc</span>,</span> +<span> secondary <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span> +<span> n <span class="op">=</span> <span class="fl">10</span>,</span> +<span> LOD <span class="op">=</span> <span class="fl">0.1</span>,</span> +<span> reps <span class="op">=</span> <span class="fl">2</span>,</span> +<span> digits <span class="op">=</span> <span class="fl">1</span>,</span> +<span> seed <span class="op">=</span> <span class="cn">NA</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>prediction</dt> +<dd><p>A prediction from a kinetic model as produced by +<code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd> + + +<dt>sdfunc</dt> +<dd><p>A function taking the predicted value as its only argument and returning a standard deviation that should be used for generating the -random error terms for this value.</p></td> - </tr> - <tr> - <th>secondary</th> - <td><p>The names of state variables that should have an initial -value of zero</p></td> - </tr> - <tr> - <th>n</th> - <td><p>The number of datasets to be generated.</p></td> - </tr> - <tr> - <th>LOD</th> - <td><p>The limit of detection (LOD). Values that are below the LOD after -adding the random error will be set to NA.</p></td> - </tr> - <tr> - <th>reps</th> - <td><p>The number of replicates to be generated within the datasets.</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>The number of digits to which the values will be rounded.</p></td> - </tr> - <tr> - <th>seed</th> - <td><p>The seed used for the generation of random numbers. If NA, the -seed is not set.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A list of datasets compatible with <code><a href='mmkin.html'>mmkin</a></code>, i.e. the -components of the list are datasets compatible with <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +random error terms for this value.</p></dd> + + +<dt>secondary</dt> +<dd><p>The names of state variables that should have an initial +value of zero</p></dd> + + +<dt>n</dt> +<dd><p>The number of datasets to be generated.</p></dd> + + +<dt>LOD</dt> +<dd><p>The limit of detection (LOD). Values that are below the LOD after +adding the random error will be set to NA.</p></dd> + +<dt>reps</dt> +<dd><p>The number of replicates to be generated within the datasets.</p></dd> + + +<dt>digits</dt> +<dd><p>The number of digits to which the values will be rounded.</p></dd> + + +<dt>seed</dt> +<dd><p>The seed used for the generation of random numbers. If NA, the +seed is not set.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the +components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p> + </div> + <div id="references"> + <h2>References</h2> <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy https://jrwb.de/posters/piacenza_2015.pdf</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># The kinetic model</span> -<span class='va'>m_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># Generate a prediction for a specific set of parameters</span> -<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> - -<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> -<span class='co'># from 2015</span> -<span class='va'>d_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO_SFO</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, - k_M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>log</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>/</span><span class='fl'>1000</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span> -<span class='co'># of 10, and generate three datasets</span> -<span class='va'>d_SFO_SFO_err</span> <span class='op'><-</span> <span class='fu'>add_err</span><span class='op'>(</span><span class='va'>d_SFO_SFO</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fl'>10</span>, n <span class='op'>=</span> <span class='fl'>3</span>, seed <span class='op'>=</span> <span class='fl'>123456789</span> <span class='op'>)</span> - -<span class='co'># Name the datasets for nicer plotting</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_SFO_SFO_err</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> - -<span class='co'># Name the model in the list of models (with only one member in this case) for</span> -<span class='co'># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span> -<span class='co'># checks</span> -<span class='co'># \dontrun{</span> -<span class='va'>f_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_SFO_SFO</span><span class='op'>)</span>, - <span class='va'>d_SFO_SFO_err</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># We would like to inspect the fit for dataset 3 more closely</span> -<span class='co'># Using double brackets makes the returned object an mkinfit object</span> -<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> -<span class='co'># and plot.mmkin is used</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_SFO_SFO</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The kinetic model</span></span></span> +<span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Generate a prediction for a specific set of parameters</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span></span></span> +<span class="r-in"><span><span class="co"># from 2015</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add an error term with a constant (independent of the value) standard deviation</span></span></span> +<span class="r-in"><span><span class="co"># of 10, and generate three datasets</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_SFO_err</span> <span class="op"><-</span> <span class="fu">add_err</span><span class="op">(</span><span class="va">d_SFO_SFO</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fl">10</span>, n <span class="op">=</span> <span class="fl">3</span>, seed <span class="op">=</span> <span class="fl">123456789</span> <span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the datasets for nicer plotting</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_SFO_SFO_err</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Name the model in the list of models (with only one member in this case) for</span></span></span> +<span class="r-in"><span><span class="co"># nicer plotting later on. Be quiet and use only one core not to offend CRAN</span></span></span> +<span class="r-in"><span><span class="co"># checks</span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"SFO-SFO"</span> <span class="op">=</span> <span class="va">m_SFO_SFO</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">d_SFO_SFO_err</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># We would like to inspect the fit for dataset 3 more closely</span></span></span> +<span class="r-in"><span><span class="co"># Using double brackets makes the returned object an mkinfit object</span></span></span> +<span class="r-in"><span><span class="co"># instead of a list of mkinfit objects, so plot.mkinfit is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># If we use single brackets, we should give two indices (model and dataset),</span></span></span> +<span class="r-in"><span><span class="co"># and plot.mmkin is used</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_SFO_SFO</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">3</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="add_err-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index 2c109cc2..1689e436 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -62,7 +62,10 @@ the model on the previous line."><meta name="robots" content="noindex"><!-- math <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index e552cc62..81b9b2e9 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index 2237a539..16bd388b 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -1,74 +1,19 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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The alternative method 'profile' is based on the profile likelihood for each parameter. The 'profile' method uses two nested optimisations and can take a very long time, even if parallelized by specifying 'cores' on unixoid platforms. The speed of the method could likely be improved by using the -method of Venzon and Moolgavkar (1988)." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +method of Venzon and Moolgavkar (1988)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -79,23 +24,21 @@ method of Venzon and Moolgavkar (1988)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -105,48 +48,50 @@ method of Venzon and Moolgavkar (1988)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Confidence intervals for parameters of mkinfit objects</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/confint.mkinfit.R" class="external-link"><code>R/confint.mkinfit.R</code></a></small> <div class="hidden name"><code>confint.mkinfit.Rd</code></div> </div> @@ -161,279 +106,301 @@ platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988).</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span> - <span class='va'>object</span>, - <span class='va'>parm</span>, - level <span class='op'>=</span> <span class='fl'>0.95</span>, - alpha <span class='op'>=</span> <span class='fl'>1</span> <span class='op'>-</span> <span class='va'>level</span>, - <span class='va'>cutoff</span>, - method <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"quadratic"</span>, <span class='st'>"profile"</span><span class='op'>)</span>, - transformed <span class='op'>=</span> <span class='cn'>TRUE</span>, - backtransform <span class='op'>=</span> <span class='cn'>TRUE</span>, - cores <span class='op'>=</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, - rel_tol <span class='op'>=</span> <span class='fl'>0.01</span>, - quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td> - </tr> - <tr> - <th>parm</th> - <td><p>A vector of names of the parameters which are to be given -confidence intervals. If missing, all parameters are considered.</p></td> - </tr> - <tr> - <th>level</th> - <td><p>The confidence level required</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The allowed error probability, overrides 'level' if specified.</p></td> - </tr> - <tr> - <th>cutoff</th> - <td><p>Possibility to specify an alternative cutoff for the difference + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> <span class="va">parm</span>,</span> +<span> level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> alpha <span class="op">=</span> <span class="fl">1</span> <span class="op">-</span> <span class="va">level</span>,</span> +<span> <span class="va">cutoff</span>,</span> +<span> method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"quadratic"</span>, <span class="st">"profile"</span><span class="op">)</span>,</span> +<span> transformed <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> backtransform <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> cores <span class="op">=</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> rel_tol <span class="op">=</span> <span class="fl">0.01</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + +<dt>parm</dt> +<dd><p>A vector of names of the parameters which are to be given +confidence intervals. If missing, all parameters are considered.</p></dd> + + +<dt>level</dt> +<dd><p>The confidence level required</p></dd> + + +<dt>alpha</dt> +<dd><p>The allowed error probability, overrides 'level' if specified.</p></dd> + + +<dt>cutoff</dt> +<dd><p>Possibility to specify an alternative cutoff for the difference in the log-likelihoods at the confidence boundary. Specifying an explicit -cutoff value overrides arguments 'level' and 'alpha'</p></td> - </tr> - <tr> - <th>method</th> - <td><p>The 'quadratic' method approximates the likelihood function at +cutoff value overrides arguments 'level' and 'alpha'</p></dd> + + +<dt>method</dt> +<dd><p>The 'quadratic' method approximates the likelihood function at the optimised parameters using the second term of the Taylor expansion, using a second derivative (hessian) contained in the object. The 'profile' method searches the parameter space for the -cutoff of the confidence intervals by means of a likelihood ratio test.</p></td> - </tr> - <tr> - <th>transformed</th> - <td><p>If the quadratic approximation is used, should it be -applied to the likelihood based on the transformed parameters?</p></td> - </tr> - <tr> - <th>backtransform</th> - <td><p>If we approximate the likelihood in terms of the +cutoff of the confidence intervals by means of a likelihood ratio test.</p></dd> + + +<dt>transformed</dt> +<dd><p>If the quadratic approximation is used, should it be +applied to the likelihood based on the transformed parameters?</p></dd> + + +<dt>backtransform</dt> +<dd><p>If we approximate the likelihood in terms of the transformed parameters, should we backtransform the parameters with -their confidence intervals?</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to be used for multicore processing. -On Windows machines, cores > 1 is currently not supported.</p></td> - </tr> - <tr> - <th>rel_tol</th> - <td><p>If the method is 'profile', what should be the accuracy +their confidence intervals?</p></dd> + + +<dt>cores</dt> +<dd><p>The number of cores to be used for multicore processing. +On Windows machines, cores > 1 is currently not supported.</p></dd> + + +<dt>rel_tol</dt> +<dd><p>If the method is 'profile', what should be the accuracy of the lower and upper bounds, relative to the estimate obtained from -the quadratic method?</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should we suppress the message "Profiling the likelihood"</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A matrix with columns giving lower and upper confidence limits for -each parameter.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> +the quadratic method?</p></dd> + + +<dt>quiet</dt> +<dd><p>Should we suppress the message "Profiling the likelihood"</p></dd> + +<dt>...</dt> +<dd><p>Not used</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A matrix with columns giving lower and upper confidence limits for +each parameter.</p> + </div> + <div id="references"> + <h2>References</h2> <p>Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications</p> <p>Pawitan Y (2013) In all likelihood - Statistical modelling and inference using likelihood. Clarendon Press, Oxford.</p> <p>Venzon DJ and Moolgavkar SH (1988) A Method for Computing Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 71.8242430 93.1600766 -#> k_parent 0.2109541 0.4440528 -#> sigma 1.9778868 7.3681380</div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f</span>, method <span class='op'>=</span> <span class='st'>"profile"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 73.0641834 92.1392181 -#> k_parent 0.2170293 0.4235348 -#> sigma 3.1307772 8.0628314</div><div class='input'> -<span class='co'># Set the number of cores for the profiling method for further examples</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/identical.html'>identical</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"NOT_CRAN"</span><span class='op'>)</span>, <span class='st'>"true"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>-</span> <span class='fl'>1</span> -<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span> - <span class='va'>n_cores</span> <span class='op'><-</span> <span class='fl'>1</span> -<span class='op'>}</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv</a></span><span class='op'>(</span><span class='st'>"TRAVIS"</span><span class='op'>)</span> <span class='op'>!=</span> <span class='st'>""</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='va'>n_cores</span> <span class='op'>=</span> <span class='fl'>1</span> - -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f_d_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> user system elapsed -#> 4.295 1.008 3.959 </div><div class='input'><span class='co'># Using more cores does not save much time here, as parent_0 takes up most of the time</span> -<span class='co'># If we additionally exclude parent_0 (the confidence of which is often of</span> -<span class='co'># minor interest), we get a nice performance improvement if we use at least 4 cores</span> -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>ci_profile_no_parent_0</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"k_parent_sink"</span>, <span class='st'>"k_parent_m1"</span>, <span class='st'>"k_m1_sink"</span>, <span class='st'>"sigma"</span><span class='op'>)</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> user system elapsed -#> 1.451 0.126 0.923 </div><div class='input'><span class='va'>ci_profile</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent_sink 0.040762501 5.549764e-02 -#> k_parent_m1 0.046786482 5.500879e-02 -#> k_m1_sink 0.003892605 6.702778e-03 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -<span class='va'>ci_quadratic_transformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841640 1.027931e+02 -#> k_parent_sink 0.041033378 5.596269e-02 -#> k_parent_m1 0.046777902 5.511931e-02 -#> k_m1_sink 0.004012217 6.897547e-03 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>ci_quadratic_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_1</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -<span class='va'>ci_quadratic_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841645 102.79312449 -#> k_parent_sink 0.040485331 0.05535491 -#> k_parent_m1 0.046611582 0.05494364 -#> k_m1_sink 0.003835483 0.00668582 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='co'># Against the expectation based on Bates and Watts (1988), the confidence</span> -<span class='co'># intervals based on the internal parameter transformation are less</span> -<span class='co'># congruent with the likelihood based intervals. Note the superiority of the</span> -<span class='co'># interval based on the untransformed fit for k_m1_sink</span> -<span class='va'>rel_diffs_transformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> -<span class='va'>rel_diffs_untransformed</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed</span> <span class='op'>-</span> <span class='va'>ci_profile</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile</span><span class='op'>)</span> -<span class='va'>rel_diffs_transformed</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent_sink TRUE FALSE -#> k_parent_m1 TRUE FALSE -#> k_m1_sink FALSE FALSE -#> sigma FALSE FALSE</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_transformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006650 0.008380 -#> k_parent_m1 0.000183 0.002010 -#> k_m1_sink 0.030700 0.029100 -#> sigma 0.055000 0.032700</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span><span class='op'>(</span><span class='va'>rel_diffs_untransformed</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.000541 0.000222 -#> k_parent_sink 0.006800 0.002570 -#> k_parent_m1 0.003740 0.001180 -#> k_m1_sink 0.014700 0.002530 -#> sigma 0.055000 0.032700</div><div class='input'> - -<span class='co'># Investigate a case with formation fractions</span> -<span class='va'>f_d_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>ci_profile_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"profile"</span>, cores <span class='op'>=</span> <span class='va'>n_cores</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='va'>ci_profile_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003640 1.027703e+02 -#> k_parent 0.090911032 1.071578e-01 -#> k_m1 0.003892606 6.702775e-03 -#> f_parent_to_m1 0.471328495 5.611550e-01 -#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -<span class='va'>ci_quadratic_transformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833578 102.79311649 -#> k_parent 0.090823771 0.10725430 -#> k_m1 0.004012219 0.00689755 -#> f_parent_to_m1 0.469118824 0.55959615 -#> sigma 2.396089689 3.85491806</div><div class='input'><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_d_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span>, transformed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -<span class='va'>ci_quadratic_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403833583 1.027931e+02 -#> k_parent 0.090491913 1.069035e-01 -#> k_m1 0.003835485 6.685823e-03 -#> f_parent_to_m1 0.469113477 5.598387e-01 -#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_transformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> -<span class='va'>rel_diffs_untransformed_ff</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span><span class='op'>(</span><span class='op'>(</span><span class='va'>ci_quadratic_untransformed_ff</span> <span class='op'>-</span> <span class='va'>ci_profile_ff</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ci_profile_ff</span><span class='op'>)</span> -<span class='co'># While the confidence interval for the parent rate constant is closer to</span> -<span class='co'># the profile based interval when using the internal parameter</span> -<span class='co'># transformation, the interval for the metabolite rate constant is 'better</span> -<span class='co'># without internal parameter transformation.</span> -<span class='va'>rel_diffs_transformed_ff</span> <span class='op'><</span> <span class='va'>rel_diffs_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 FALSE FALSE -#> k_parent TRUE TRUE -#> k_m1 FALSE FALSE -#> f_parent_to_m1 TRUE FALSE -#> sigma TRUE FALSE</div><div class='input'><span class='va'>rel_diffs_transformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408690 0.0002217233 -#> k_parent 0.0009598532 0.0009001864 -#> k_m1 0.0307283041 0.0290588361 -#> f_parent_to_m1 0.0046881769 0.0027780063 -#> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='va'>rel_diffs_untransformed_ff</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408689 0.0002217232 -#> k_parent 0.0046102156 0.0023732281 -#> k_m1 0.0146740690 0.0025291820 -#> f_parent_to_m1 0.0046995211 0.0023457712 -#> sigma 0.0550252516 0.0327066836</div><div class='input'> -<span class='co'># The profiling for the following fit does not finish in a reasonable time,</span> -<span class='co'># therefore we use the quadratic approximation</span> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>DFOP_par_c</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>f_tc_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>DFOP_par_c</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, - error_model_algorithm <span class='op'>=</span> <span class='st'>"direct"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596039609 106.19954892 -#> k_M1 0.037605368 0.04490762 -#> k_M2 0.008568731 0.01087676 -#> f_parent_to_M1 0.021462489 0.62023882 -#> f_parent_to_M2 0.015165617 0.37975348 -#> k1 0.273897348 0.33388101 -#> k2 0.018614554 0.02250378 -#> g 0.671943411 0.73583305 -#> sigma_low 0.251283495 0.83992077 -#> rsd_high 0.040411024 0.07662008</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span><span class='op'>(</span><span class='va'>f_tc_2</span>, <span class='st'>"parent_0"</span>, method <span class='op'>=</span> <span class='st'>"quadratic"</span><span class='op'>)</span> -</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59604 106.1995</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 71.8242430 93.1600766</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2109541 0.4440528</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.9778868 7.3681380</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"profile"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 73.0641834 92.1392181</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.2170293 0.4235348</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.1307772 8.0628314</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Set the number of cores for the profiling method for further examples</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"NOT_CRAN"</span><span class="op">)</span>, <span class="st">"true"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">n_cores</span> <span class="op"><-</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.getenv.html" class="external-link">Sys.getenv</a></span><span class="op">(</span><span class="st">"TRAVIS"</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="va">n_cores</span> <span class="op">=</span> <span class="fl">1</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"min"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 3.811 0.004 3.815 </span> +<span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> +<span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> +<span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile_no_parent_0</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 2.313 0.004 2.318 </span> +<span class="r-in"><span><span class="va">ci_profile</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040762501 5.549764e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046786482 5.500879e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003892605 6.702778e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841640 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.041033378 5.596269e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046777902 5.511931e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.004012217 6.897547e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403841645 102.79312449</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.040485331 0.05535491</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.046611582 0.05494364</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.003835483 0.00668582</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> +<span class="r-in"><span><span class="co"># Against the expectation based on Bates and Watts (1988), the confidence</span></span></span> +<span class="r-in"><span><span class="co"># intervals based on the internal parameter transformation are less</span></span></span> +<span class="r-in"><span><span class="co"># congruent with the likelihood based intervals. Note the superiority of the</span></span></span> +<span class="r-in"><span><span class="co"># interval based on the untransformed fit for k_m1_sink</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed</span> <span class="op">-</span> <span class="va">ci_profile</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> sigma FALSE FALSE</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_transformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006650 0.008380</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.000183 0.002010</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.030700 0.029100</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">signif</a></span><span class="op">(</span><span class="va">rel_diffs_untransformed</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.000541 0.000222</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.006800 0.002570</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.003740 0.001180</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.014700 0.002530</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.055000 0.032700</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Investigate a case with formation fractions</span></span></span> +<span class="r-in"><span><span class="va">f_d_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_profile_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> +<span class="r-in"><span><span class="va">ci_profile_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090911032 1.071578e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003892606 6.702775e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.471328495 5.611550e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.535612399 3.985263e+00</span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_transformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833578 102.79311649</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090823771 0.10725430</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.004012219 0.00689755</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469118824 0.55959615</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.85491806</span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span>, transformed <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ci_quadratic_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 96.403833583 1.027931e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.090491913 1.069035e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.003835485 6.685823e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.469113477 5.598387e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.396089689 3.854918e+00</span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_transformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="op">(</span><span class="va">ci_quadratic_untransformed_ff</span> <span class="op">-</span> <span class="va">ci_profile_ff</span><span class="op">)</span><span class="op">/</span><span class="va">ci_profile_ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># While the confidence interval for the parent rate constant is closer to</span></span></span> +<span class="r-in"><span><span class="co"># the profile based interval when using the internal parameter</span></span></span> +<span class="r-in"><span><span class="co"># transformation, the interval for the metabolite rate constant is 'better</span></span></span> +<span class="r-in"><span><span class="co"># without internal parameter transformation.</span></span></span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span> <span class="op"><</span> <span class="va">rel_diffs_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent TRUE TRUE</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 FALSE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 TRUE FALSE</span> +<span class="r-out co"><span class="r-pr">#></span> sigma TRUE FALSE</span> +<span class="r-in"><span><span class="va">rel_diffs_transformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408690 0.0002217233</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0009598532 0.0009001864</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0307283041 0.0290588361</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046881769 0.0027780063</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> +<span class="r-in"><span><span class="va">rel_diffs_untransformed_ff</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 0.0005408689 0.0002217232</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0046102156 0.0023732281</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0146740690 0.0025291820</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.0046995211 0.0023457712</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 0.0550252516 0.0327066836</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The profiling for the following fit does not finish in a reasonable time,</span></span></span> +<span class="r-in"><span><span class="co"># therefore we use the quadratic approximation</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">DFOP_par_c</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">f_tc_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">DFOP_par_c</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> +<span class="r-in"><span> error_model_algorithm <span class="op">=</span> <span class="st">"direct"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.596039609 106.19954892</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.037605368 0.04490762</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.008568731 0.01087676</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.021462489 0.62023882</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.015165617 0.37975348</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.273897348 0.33388101</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.018614554 0.02250378</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.671943411 0.73583305</span> +<span class="r-out co"><span class="r-pr">#></span> sigma_low 0.251283495 0.83992077</span> +<span class="r-out co"><span class="r-pr">#></span> rsd_high 0.040411024 0.07662008</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_tc_2</span>, <span class="st">"parent_0"</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 94.59604 106.1995</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index 5d5870fe..e2a42873 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -125,8 +131,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.401 1.000 0.401 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.654 1.631 0.654 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.458 1.000 0.458 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.713 1.557 0.713 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -139,8 +145,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.843 1.000 0.843 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.445 1.714 1.445 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.884 1.000 0.883 0.000 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.526 1.726 1.522 0.004 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/dev/reference/dimethenamid_2018-1.png b/docs/dev/reference/dimethenamid_2018-1.png Binary files differindex 4300b0c0..c8b05bf5 100644 --- a/docs/dev/reference/dimethenamid_2018-1.png +++ b/docs/dev/reference/dimethenamid_2018-1.png diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 2454a609..96ec73c6 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -49,19 +49,25 @@ constrained by data protection regulations."><meta name="robots" content="noinde <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -180,17 +186,15 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># influence of ill-defined rate constants that have</span></span></span> <span class="r-in"><span><span class="co"># extremely small values:</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># If we disregards ill-defined rate constants, the results</span></span></span> <span class="r-in"><span><span class="co"># look more plausible, but the truth is likely to be in</span></span></span> <span class="r-in"><span><span class="co"># between these variants</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-2.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="dimethenamid_2018-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># We can also specify a default value for the failing</span></span></span> <span class="r-in"><span><span class="co"># log parameters, to mimic FOCUS guidance</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="mixed.html">mixed</a></span><span class="op">(</span><span class="va">dmta_sfo_sfo3p_tc</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> <span class="r-in"><span> default_log_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">2</span><span class="op">)</span><span class="op">/</span><span class="fl">1000</span><span class="op">)</span></span></span> -<span class="r-plt img"><img src="dimethenamid_2018-3.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="co"># As these attempts are not satisfying, we use nonlinear mixed-effects models</span></span></span> <span class="r-in"><span><span class="co"># f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc)</span></span></span> <span class="r-in"><span><span class="co"># nlme reaches maxIter = 50 without convergence</span></span></span> @@ -200,11 +204,11 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># graphics device used)</span></span></span> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri Sep 16 10:29:07 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri Sep 16 10:29:07 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:05:16 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:05:16 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -217,7 +221,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 797.539 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 819.725 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -235,69 +239,79 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 2276 2272 -1120</span> +<span class="r-out co"><span class="r-pr">#></span> 2276 2273 -1120</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.5943 84.3961 92.7925</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0466 -3.5609 -2.5322</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0684 -4.9340 -3.2029</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8628 -4.2627 -3.4628</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9803 -4.4804 -3.4801</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1304 -0.2186 0.4795</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1490 -0.2559 0.5540</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3970 -1.6976 -1.0964</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.3192 83.8656 92.7729</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA -3.0530 -3.5686 -2.5373</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -4.0620 -4.9202 -3.2038</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -3.8633 -4.2668 -3.4598</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -3.9731 -4.4763 -3.4699</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 0.1346 -0.2150 0.4841</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 0.1449 -0.2593 0.5491</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -1.3882 -1.7011 -1.0753</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0309 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0231 -0.0031 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0381 -0.0048 0.0039 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0251 -0.0031 0.0021 0.0830 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0417 -0.0437 0.0328 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0270 -0.0909 -0.0361 </span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1832 -0.0135 0.0434 0.0804 0.0395 -0.0070 0.0059 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_DMTA 0.0303 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M23 -0.0229 -0.0032 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M27 -0.0372 -0.0049 0.0041 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M31 -0.0245 -0.0032 0.0022 0.0815 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_1 -0.0046 -0.0006 0.0415 -0.0433 0.0324 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_2 -0.0008 -0.0002 0.0214 -0.0267 -0.0893 -0.0361 </span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_ilr_3 -0.1755 -0.0135 0.0423 0.0775 0.0377 -0.0066 0.0060 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.3651 -0.9649 7.6951</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6415 0.2774 1.0055</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0176 0.3809 1.6543</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4538 0.1522 0.7554</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5684 0.1905 0.9464</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4111 0.1524 0.6699</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4788 0.1808 0.7768</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3501 0.1316 0.5685</span> +<span class="r-out co"><span class="r-pr">#></span> SD.DMTA_0 3.7280 -0.6951 8.1511</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_DMTA 0.6431 0.2781 1.0080</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M23 1.0096 0.3782 1.6409</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M27 0.4583 0.1541 0.7625</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_M31 0.5738 0.1942 0.9533</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_1 0.4119 0.1528 0.6709</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_2 0.4780 0.1806 0.7754</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_DMTA_ilr_3 0.3657 0.1383 0.5931</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> -<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.9349 0.8409 1.029</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.1344 0.1178 0.151</span> +<span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.9156 0.8229 1.0084</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.1383 0.1215 0.1551</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.59431 84.396147 92.79246</span> -<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04752 0.028413 0.07948</span> -<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01710 0.007198 0.04064</span> -<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02101 0.014084 0.03134</span> -<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01868 0.011329 0.03080</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14498 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12056 NA NA</span> -<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11015 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_0 88.31924 83.865625 92.77286</span> +<span class="r-out co"><span class="r-pr">#></span> k_DMTA 0.04722 0.028196 0.07908</span> +<span class="r-out co"><span class="r-pr">#></span> k_M23 0.01721 0.007298 0.04061</span> +<span class="r-out co"><span class="r-pr">#></span> k_M27 0.02100 0.014027 0.03144</span> +<span class="r-out co"><span class="r-pr">#></span> k_M31 0.01882 0.011375 0.03112</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M23 0.14608 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M27 0.12077 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_DMTA_to_M31 0.11123 NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1450</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1206</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1101</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6243</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M23 0.1461</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M27 0.1208</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_M31 0.1112</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA_sink 0.6219</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> -<span class="r-out co"><span class="r-pr">#></span> DMTA 14.59 48.45</span> -<span class="r-out co"><span class="r-pr">#></span> M23 40.52 134.62</span> -<span class="r-out co"><span class="r-pr">#></span> M27 32.99 109.60</span> -<span class="r-out co"><span class="r-pr">#></span> M31 37.11 123.26</span> +<span class="r-out co"><span class="r-pr">#></span> DMTA 14.68 48.76</span> +<span class="r-out co"><span class="r-pr">#></span> M23 40.27 133.76</span> +<span class="r-out co"><span class="r-pr">#></span> M27 33.01 109.65</span> +<span class="r-out co"><span class="r-pr">#></span> M31 36.84 122.38</span> <span class="r-in"><span><span class="co"># As the confidence interval for the random effects of DMTA_0</span></span></span> <span class="r-in"><span><span class="co"># includes zero, we could try an alternative model without</span></span></span> <span class="r-in"><span><span class="co"># such random effects</span></span></span> diff --git a/docs/dev/reference/ds_mixed-1.png b/docs/dev/reference/ds_mixed-1.png Binary files differnew file mode 100644 index 00000000..a7f5c395 --- /dev/null +++ b/docs/dev/reference/ds_mixed-1.png diff --git a/docs/dev/reference/ds_mixed.html b/docs/dev/reference/ds_mixed.html new file mode 100644 index 00000000..09a6cc8c --- /dev/null +++ b/docs/dev/reference/ds_mixed.html @@ -0,0 +1,240 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand 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class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ds_mixed.R" class="external-link"><code>R/ds_mixed.R</code></a></small> + <div class="hidden name"><code>ds_mixed.Rd</code></div> + </div> + + <div class="ref-description"> + <p>The R code used to create this data object is installed with this package in +the 'dataset_generation' directory.</p> + </div> + + + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">sfo_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">sfo_mmkin</span>, no_random_effect <span class="op">=</span> <span class="st">"parent_0"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_saem</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="ds_mixed-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is the code used to generate the datasets</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/cat.html" class="external-link">cat</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/readLines.html" class="external-link">readLines</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"dataset_generation/ds_mixed.R"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span><span class="op">)</span>, sep <span class="op">=</span> <span class="st">"\n"</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> # Synthetic data for hierarchical kinetic models</span> +<span class="r-out co"><span class="r-pr">#></span> # Refactored version of the code previously in tests/testthat/setup_script.R</span> +<span class="r-out co"><span class="r-pr">#></span> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it</span> +<span class="r-out co"><span class="r-pr">#></span> # is always 15 for consistency</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> library(mkin) # We use mkinmod and mkinpredict</span> +<span class="r-out co"><span class="r-pr">#></span> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)</span> +<span class="r-out co"><span class="r-pr">#></span> n <- 15</span> +<span class="r-out co"><span class="r-pr">#></span> log_sd <- 0.3</span> +<span class="r-out co"><span class="r-pr">#></span> err_1 = list(const = 1, prop = 0.05)</span> +<span class="r-out co"><span class="r-pr">#></span> tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop)</span> +<span class="r-out co"><span class="r-pr">#></span> const <- function(value) 2</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> SFO <- mkinmod(parent = mkinsub("SFO"))</span> +<span class="r-out co"><span class="r-pr">#></span> sfo_pop <- list(parent_0 = 100, k_parent = 0.03)</span> +<span class="r-out co"><span class="r-pr">#></span> sfo_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_sfo <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(SFO, sfo_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = sfo_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_sfo, "pop") <- sfo_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_sfo, "parms") <- sfo_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> FOMC <- mkinmod(parent = mkinsub("FOMC"))</span> +<span class="r-out co"><span class="r-pr">#></span> fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8)</span> +<span class="r-out co"><span class="r-pr">#></span> fomc_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> alpha = rlnorm(n, log(fomc_pop$alpha), 0.4),</span> +<span class="r-out co"><span class="r-pr">#></span> beta = rlnorm(n, log(fomc_pop$beta), 0.2)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_fomc <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(FOMC, fomc_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = fomc_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_fomc, "pop") <- fomc_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_fomc, "parms") <- fomc_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP <- mkinmod(parent = mkinsub("DFOP"))</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(dfop_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(dfop_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd))))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(DFOP, dfop_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = dfop_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, tc, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop, "pop") <- dfop_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop, "parms") <- dfop_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> HS <- mkinmod(parent = mkinsub("HS"))</span> +<span class="r-out co"><span class="r-pr">#></span> hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15)</span> +<span class="r-out co"><span class="r-pr">#></span> hs_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(hs_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(hs_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> tb = rlnorm(n, log(hs_pop$tb), 0.1)))</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_hs <- lapply(1:n, function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> ds_mean <- mkinpredict(HS, hs_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = hs_pop$parent_0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds_mean, const, n = 1)[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_hs, "pop") <- hs_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_hs, "parms") <- hs_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP_SFO <- mkinmod(</span> +<span class="r-out co"><span class="r-pr">#></span> parent = mkinsub("DFOP", "m1"),</span> +<span class="r-out co"><span class="r-pr">#></span> m1 = mkinsub("SFO"),</span> +<span class="r-out co"><span class="r-pr">#></span> quiet = TRUE)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_sfo_pop <- list(parent_0 = 100,</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 = 0.007, f_parent_to_m1 = 0.5,</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = 0.1, k2 = 0.02, g = 0.5)</span> +<span class="r-out co"><span class="r-pr">#></span> dfop_sfo_parms <- as.matrix(data.frame(</span> +<span class="r-out co"><span class="r-pr">#></span> k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd),</span> +<span class="r-out co"><span class="r-pr">#></span> g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)),</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 = plogis(rnorm(n,</span> +<span class="r-out co"><span class="r-pr">#></span> qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)),</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd)))</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop_sfo_mean <- lapply(1:n,</span> +<span class="r-out co"><span class="r-pr">#></span> function(i) {</span> +<span class="r-out co"><span class="r-pr">#></span> mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ],</span> +<span class="r-out co"><span class="r-pr">#></span> c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times)</span> +<span class="r-out co"><span class="r-pr">#></span> }</span> +<span class="r-out co"><span class="r-pr">#></span> )</span> +<span class="r-out co"><span class="r-pr">#></span> set.seed(123456)</span> +<span class="r-out co"><span class="r-pr">#></span> ds_dfop_sfo <- lapply(ds_dfop_sfo_mean, function(ds) {</span> +<span class="r-out co"><span class="r-pr">#></span> add_err(ds,</span> +<span class="r-out co"><span class="r-pr">#></span> sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2),</span> +<span class="r-out co"><span class="r-pr">#></span> n = 1, secondary = "m1")[[1]]</span> +<span class="r-out co"><span class="r-pr">#></span> })</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop_sfo, "pop") <- dfop_sfo_pop</span> +<span class="r-out co"><span class="r-pr">#></span> attr(ds_dfop_sfo, "parms") <- dfop_sfo_parms</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)</span> +</code></pre></div> + </div> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> +</div> + + + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> +</div> + + </footer></div> + + + + + + + </body></html> + diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index e8198521..f8064098 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -65,7 +65,10 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/experimental_data_for_UBA-1.png b/docs/dev/reference/experimental_data_for_UBA-1.png Binary files differindex 33946ded..b7b4d63b 100644 --- a/docs/dev/reference/experimental_data_for_UBA-1.png +++ b/docs/dev/reference/experimental_data_for_UBA-1.png diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html index 9904370f..a51ace27 100644 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ b/docs/dev/reference/experimental_data_for_UBA.html @@ -1,46 +1,5 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, 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Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some results are shown here do not imply a license to use them in the context of @@ -68,28 +27,14 @@ Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D the exception of the day three sampling of metabolite A2, which was set to one half of the LOD reported to be 1% AR. Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl - (United Kingdom, 2014, p. 81)." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> + (United Kingdom, 2014, p. 81)."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -100,23 +45,21 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -126,44 +69,46 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Experimental datasets used for development and testing of error models</h1> @@ -203,30 +148,33 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> </div> - <pre class="usage"><span class='va'>experimental_data_for_UBA_2019</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, + each containing, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> <p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p> <p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> -<p>FOCUS (2014) “Generic guidance for Estimating Persistence and +<p>FOCUS (2014) “Generic guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU - Registration” Report of the FOCUS Work Group on Degradation Kinetics, + Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 - <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> <p>Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate and Behaviour</p> <p>Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the @@ -236,70 +184,75 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed Decision of the United Kingdom made to the European Commission under Regulation (EC) No. 1141/2010 for renewal of an active substance</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> - -<span class='co'># Model definitions</span> -<span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>sfo_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>dfop_sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"A1"</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span> -<span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>d_1_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>d_1_2</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Soil"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>)</span> - - -<span class='va'>f_1_2_tc</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo_sfo</span><span class='op'>)</span>, <span class='va'>d_1_2</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_1_2_tc</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> -</div><div class='img'><img src='experimental_data_for_UBA-1.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># }</span></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Model definitions</span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">sfo_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">dfop_sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"A1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">d_1_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">d_1_2</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Soil"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_1_2_tc</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO-SFO"</span> <span class="op">=</span> <span class="va">dfop_sfo_sfo</span><span class="op">)</span>, <span class="va">d_1_2</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_1_2_tc</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="experimental_data_for_UBA-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html index 852e00a0..b556df04 100644 --- a/docs/dev/reference/f_time_norm_focus.html +++ 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-73,23 +18,21 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Normalisation factors for aerobic soil degradation according to FOCUS guidance</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/f_time_norm_focus.R'><code>R/f_time_norm_focus.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/f_time_norm_focus.R" class="external-link"><code>R/f_time_norm_focus.R</code></a></small> <div class="hidden name"><code>f_time_norm_focus.Rd</code></div> </div> @@ -149,137 +94,138 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)." /> in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p> </div> - <pre class="usage"><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for numeric</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> - <span class='va'>object</span>, - moisture <span class='op'>=</span> <span class='cn'>NA</span>, - field_moisture <span class='op'>=</span> <span class='cn'>NA</span>, - temperature <span class='op'>=</span> <span class='va'>object</span>, - Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, - walker <span class='op'>=</span> <span class='fl'>0.7</span>, - f_na <span class='op'>=</span> <span class='cn'>NA</span>, - <span class='va'>...</span> -<span class='op'>)</span> - -<span class='co'># S3 method for mkindsg</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span> - <span class='va'>object</span>, - study_moisture_ref_source <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"auto"</span>, <span class='st'>"meta"</span>, <span class='st'>"focus"</span><span class='op'>)</span>, - Q10 <span class='op'>=</span> <span class='fl'>2.58</span>, - walker <span class='op'>=</span> <span class='fl'>0.7</span>, - f_na <span class='op'>=</span> <span class='cn'>NA</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object containing information used for the calculations</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Currently not used</p></td> - </tr> - <tr> - <th>moisture</th> - <td><p>Numeric vector of moisture contents in \% w/w</p></td> - </tr> - <tr> - <th>field_moisture</th> - <td><p>Numeric vector of moisture contents at field capacity -(pF2) in \% w/w</p></td> - </tr> - <tr> - <th>temperature</th> - <td><p>Numeric vector of temperatures in °C</p></td> - </tr> - <tr> - <th>Q10</th> - <td><p>The Q10 value used for temperature normalisation</p></td> - </tr> - <tr> - <th>walker</th> - <td><p>The Walker exponent used for moisture normalisation</p></td> - </tr> - <tr> - <th>f_na</th> - <td><p>The factor to use for NA values. If set to NA, only factors -for complete cases will be returned.</p></td> - </tr> - <tr> - <th>study_moisture_ref_source</th> - <td><p>Source for the reference value + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for numeric</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> field_moisture <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> temperature <span class="op">=</span> <span class="va">object</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkindsg</span></span> +<span><span class="fu">f_time_norm_focus</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> study_moisture_ref_source <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"auto"</span>, <span class="st">"meta"</span>, <span class="st">"focus"</span><span class="op">)</span>,</span> +<span> Q10 <span class="op">=</span> <span class="fl">2.58</span>,</span> +<span> walker <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> f_na <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object containing information used for the calculations</p></dd> + + +<dt>...</dt> +<dd><p>Currently not used</p></dd> + + +<dt>moisture</dt> +<dd><p>Numeric vector of moisture contents in \% w/w</p></dd> + + +<dt>field_moisture</dt> +<dd><p>Numeric vector of moisture contents at field capacity +(pF2) in \% w/w</p></dd> + + +<dt>temperature</dt> +<dd><p>Numeric vector of temperatures in °C</p></dd> + + +<dt>Q10</dt> +<dd><p>The Q10 value used for temperature normalisation</p></dd> + + +<dt>walker</dt> +<dd><p>The Walker exponent used for moisture normalisation</p></dd> + + +<dt>f_na</dt> +<dd><p>The factor to use for NA values. If set to NA, only factors +for complete cases will be returned.</p></dd> + + +<dt>study_moisture_ref_source</dt> +<dd><p>Source for the reference value used to calculate the study moisture. If 'auto', preference is given to a reference moisture given in the meta information, otherwise -the focus soil moisture for the soil class is used</p></td> - </tr> - </table> +the focus soil moisture for the soil class is used</p></dd> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence +</dl></div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> -FOCUS (2014) “Generic guidance for Estimating Persistence +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a> +FOCUS (2014) “Generic guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p><a href='focus_soil_moisture.html'>focus_soil_moisture</a></p></div> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='fl'>25</span>, <span class='fl'>20</span>, <span class='fl'>25</span><span class='op'>)</span> <span class='co'># 1.37, compare FOCUS 2014 p. 184</span> -</div><div class='output co'>#> [1] 1.373956</div><div class='input'> -<span class='va'>D24_2014</span><span class='op'>$</span><span class='va'>meta</span> -</div><div class='output co'>#> study usda_soil_type study_moisture_ref_type -#> Mississippi Cohen 1991 Silt loam <NA> -#> Fayette Liu and Adelfinskaya 2011 Silt loam pF1 -#> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1 -#> Site E1 Liu and Adelfinskaya 2011 Loam pF1 -#> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1 -#> rel_moisture temperature -#> Mississippi NA 25 -#> Fayette 0.5 20 -#> RefSol 03-G 0.5 20 -#> Site E1 0.5 20 -#> Site I2 0.5 20</div><div class='input'><span class='co'># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span> -<span class='co'># temperature only normalisation as in the EU evaluation</span> -<span class='fu'>f_time_norm_focus</span><span class='op'>(</span><span class='va'>D24_2014</span>, study_moisture_ref_source <span class='op'>=</span> <span class='st'>"focus"</span>, f_na <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> $time_norm was set to -#> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124</div></pre> +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><a href="focus_soil_moisture.html">focus_soil_moisture</a></p></div> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">D24_2014</span><span class="op">$</span><span class="va">meta</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> study usda_soil_type study_moisture_ref_type</span> +<span class="r-out co"><span class="r-pr">#></span> Mississippi Cohen 1991 Silt loam <NA></span> +<span class="r-out co"><span class="r-pr">#></span> Fayette Liu and Adelfinskaya 2011 Silt loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> Site E1 Liu and Adelfinskaya 2011 Loam pF1</span> +<span class="r-out co"><span class="r-pr">#></span> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1</span> +<span class="r-out co"><span class="r-pr">#></span> rel_moisture temperature</span> +<span class="r-out co"><span class="r-pr">#></span> Mississippi NA 25</span> +<span class="r-out co"><span class="r-pr">#></span> Fayette 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> RefSol 03-G 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> Site E1 0.5 20</span> +<span class="r-out co"><span class="r-pr">#></span> Site I2 0.5 20</span> +<span class="r-in"><span><span class="co"># No moisture normalisation in the first dataset, so we use f_na = 1 to get</span></span></span> +<span class="r-in"><span><span class="co"># temperature only normalisation as in the EU evaluation</span></span></span> +<span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">D24_2014</span>, study_moisture_ref_source <span class="op">=</span> <span class="st">"focus"</span>, f_na <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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The table assumes field capacity +corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/focus_soil_moisture.R'><code>R/focus_soil_moisture.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/focus_soil_moisture.R" class="external-link"><code>R/focus_soil_moisture.R</code></a></small> <div class="hidden name"><code>focus_soil_moisture.Rd</code></div> </div> @@ -149,58 +94,60 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5." /> corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.</p> </div> - <pre class="usage"><span class='va'>focus_soil_moisture</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">focus_soil_moisture</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A matrix with upper case USDA soil classes as row names, and water tension ('pF1', 'pF2', 'pF 2.5') as column names</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment -Version 2.2, May 2014 <a href='https://esdac.jrc.ec.europa.eu/projects/ground-water'>https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>focus_soil_moisture</span> -</div><div class='output co'>#> pF1 pF2 pF2.5 -#> Sand 24 12 7 -#> Loamy sand 24 14 9 -#> Sandy loam 27 19 15 -#> Sandy clay loam 28 22 18 -#> Clay loam 32 28 25 -#> Loam 31 25 21 -#> Silt loam 32 26 21 -#> Silty clay loam 34 30 27 -#> Silt 31 27 21 -#> Sandy clay 41 35 31 -#> Silty clay 44 40 36 -#> Clay 53 48 43</div></pre> +Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-water" class="external-link">https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">focus_soil_moisture</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> pF1 pF2 pF2.5</span> +<span class="r-out co"><span class="r-pr">#></span> Sand 24 12 7</span> +<span class="r-out co"><span class="r-pr">#></span> Loamy sand 24 14 9</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy loam 27 19 15</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy clay loam 28 22 18</span> +<span class="r-out co"><span class="r-pr">#></span> Clay loam 32 28 25</span> +<span class="r-out co"><span class="r-pr">#></span> Loam 31 25 21</span> +<span class="r-out co"><span class="r-pr">#></span> Silt loam 32 26 21</span> +<span class="r-out co"><span class="r-pr">#></span> Silty clay loam 34 30 27</span> +<span class="r-out co"><span class="r-pr">#></span> Silt 31 27 21</span> +<span class="r-out co"><span class="r-pr">#></span> Sandy clay 41 35 31</span> +<span class="r-out co"><span class="r-pr">#></span> Silty clay 44 40 36</span> +<span class="r-out co"><span class="r-pr">#></span> Clay 53 48 43</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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+<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Retrieve a degradation function from the mmkin namespace</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> <div class="hidden name"><code>get_deg_func.Rd</code></div> </div> @@ -147,39 +92,39 @@ <p>Retrieve a degradation function from the mmkin namespace</p> </div> - <pre class="usage"><span class='fu'>get_deg_func</span><span class='op'>(</span><span class='op'>)</span></pre> - + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_deg_func</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="value"> + <h2>Value</h2> + - <p>A function that was likely previously assigned from within +<p>A function that was likely previously assigned from within nlme.mmkin</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index c0de4115..8fe71568 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ without parameter transformations is used."><meta name="robots" content="noindex <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 452647d6..c1396303 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Function to perform isometric log-ratio transformation — ilr • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ transformations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ transformations." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to perform isometric log-ratio transformation</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ilr.R" class="external-link"><code>R/ilr.R</code></a></small> <div class="hidden name"><code>ilr.Rd</code></div> </div> @@ -149,86 +94,100 @@ transformations." /> transformations.</p> </div> - <pre class="usage"><span class='fu'>ilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> - -<span class='fu'>invilr</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>A numeric vector. Naturally, the forward transformation is only -sensible for vectors with all elements being greater than zero.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>A numeric vector. Naturally, the forward transformation is only +sensible for vectors with all elements being greater than zero.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <p>The result of the forward or backward transformation. The returned +<p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Another implementation can be found in R package + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>René Lehmann and Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># Order matters</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -1.628174 -2.820079</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1.628174 2.820079</div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0 0</div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] -0.2034219 0.1174457</div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'>ilr</span><span class='op'>(</span><span class='fl'>2.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.70 0.29 0.01</div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> -<span class='fu'>invilr</span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01</div><div class='input'><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04</div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='fu'>invilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='op'>-</span><span class='fl'>10</span>, <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 1</div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> -<span class='va'>a</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>b</span> <span class='op'><-</span> <span class='fu'>invilr</span><span class='op'>(</span><span class='va'>a</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>)</span> <span class='co'># Four elements</span> -</div><div class='output co'>#> [1] 4</div><div class='input'><span class='fu'>ilr</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='fl'>1</span> <span class='op'>-</span> <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span><span class='op'>(</span><span class='va'>b</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># Gives c(0.1, 0.3, 0.5)</span> -</div><div class='output co'>#> [1] 0.1 0.3 0.5</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Order matters</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -1.628174 -2.820079</span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">10</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1.628174 2.820079</span> +<span class="r-in"><span><span class="co"># Equal entries give ilr transformations with zeros as elements</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">3</span>, <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0 0</span> +<span class="r-in"><span><span class="co"># Almost equal entries give small numbers</span></span></span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.3</span>, <span class="fl">0.4</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] -0.2034219 0.1174457</span> +<span class="r-in"><span><span class="co"># Only the ratio between the numbers counts, not their sum</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu">ilr</span><span class="op">(</span><span class="fl">2.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.7</span>, <span class="fl">0.29</span>, <span class="fl">0.01</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.70 0.29 0.01</span> +<span class="r-in"><span><span class="co"># Inverse transformation of larger numbers gives unequal elements</span></span></span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="op">-</span><span class="fl">10</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.213536e-07 9.999993e-01</span> +<span class="r-in"><span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 7.207415e-07 9.991507e-01 8.486044e-04</span> +<span class="r-in"><span><span class="co"># The sum of the elements of the inverse ilr is 1</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="fu">invilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="op">-</span><span class="fl">10</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 1</span> +<span class="r-in"><span><span class="co"># This is why we do not need all elements of the inverse transformation to go back:</span></span></span> +<span class="r-in"><span><span class="va">a</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">b</span> <span class="op"><-</span> <span class="fu">invilr</span><span class="op">(</span><span class="va">a</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">b</span><span class="op">)</span> <span class="co"># Four elements</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 4</span> +<span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="fl">1</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">b</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="co"># Gives c(0.1, 0.3, 0.5)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.1 0.3 0.5</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 5a0ec596..794126cf 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -268,9 +268,9 @@ degradation models and one or more error models</p></td> <p class="section-desc"></p> </th> </tr></tbody><tbody><tr><td> - <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> + <p><code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> </p> </td> - <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> + <td><p>Synthetic data for hierarchical kinetic degradation models</p></td> </tr><tr><td> <p><code><a href="D24_2014.html">D24_2014</a></code> </p> </td> @@ -328,6 +328,10 @@ degradation models and one or more error models</p></td> </td> <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> </tr><tr><td> + <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> + </td> + <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> + </tr><tr><td> <p><code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> </p> </td> <td><p>A dataset class for mkin</p></td> diff --git a/docs/dev/reference/intervals.saem.mmkin.html b/docs/dev/reference/intervals.saem.mmkin.html index ee714ad0..e67d8da0 100644 --- a/docs/dev/reference/intervals.saem.mmkin.html +++ b/docs/dev/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html index 314cb923..27e55455 100644 --- a/docs/dev/reference/llhist.html +++ b/docs/dev/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/loftest-1.png b/docs/dev/reference/loftest-1.png Binary files differindex d6006ecc..f1dc5fa7 100644 --- a/docs/dev/reference/loftest-1.png +++ b/docs/dev/reference/loftest-1.png diff --git a/docs/dev/reference/loftest-2.png b/docs/dev/reference/loftest-2.png Binary files differindex 4d0dc551..3f1015a9 100644 --- a/docs/dev/reference/loftest-2.png +++ b/docs/dev/reference/loftest-2.png diff --git a/docs/dev/reference/loftest-3.png b/docs/dev/reference/loftest-3.png Binary files differindex 6afd084b..d897c363 100644 --- a/docs/dev/reference/loftest-3.png +++ b/docs/dev/reference/loftest-3.png diff --git a/docs/dev/reference/loftest-4.png b/docs/dev/reference/loftest-4.png Binary files differindex f94eede1..ac44c162 100644 --- a/docs/dev/reference/loftest-4.png +++ b/docs/dev/reference/loftest-4.png diff --git a/docs/dev/reference/loftest-5.png b/docs/dev/reference/loftest-5.png Binary files differindex 43460a65..0847bbec 100644 --- a/docs/dev/reference/loftest-5.png +++ b/docs/dev/reference/loftest-5.png diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html index 9dbd547d..57bd3ee5 100644 --- a/docs/dev/reference/loftest.html +++ b/docs/dev/reference/loftest.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta 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It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test -lrtest.default from the lmtest package." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +lrtest.default from the lmtest package."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ lrtest.default from the lmtest package." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,48 +44,50 @@ lrtest.default from the lmtest package." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Lack-of-fit test for models fitted to data with replicates</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/loftest.R'><code>R/loftest.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/loftest.R" class="external-link"><code>R/loftest.R</code></a></small> <div class="hidden name"><code>loftest.Rd</code></div> </div> @@ -150,216 +95,231 @@ lrtest.default from the lmtest package." /> <p>This is a generic function with a method currently only defined for mkinfit objects. It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test -<code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> from the lmtest package.</p> +<code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> from the lmtest package.</p> </div> - <pre class="usage"><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='co'># S3 method for mkinfit</span> -<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A model object with a defined loftest method</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A model object with a defined loftest method</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +<dt>...</dt> +<dd><p>Not used</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The anova model is interpreted as the simplest form of an mkinfit model, assuming only a constant variance about the means, but not enforcing any structure of the means, so we have one model parameter for every mean of replicate samples.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>lrtest</p></div> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>lrtest</p></div> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>test_data</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span> -<span class='va'>sfo_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We see a clear pattern in the residuals</span> -</div><div class='img'><img src='loftest-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_fit</span><span class='op'>)</span> <span class='co'># We have a clear lack of fit</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 10 -40.710 -#> 2 3 -63.954 -7 46.487 7.027e-08 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='co'># We try a different model (the one that was used to generate the data)</span> -<span class='va'>dfop_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># We don't see systematic deviations, but heteroscedastic residuals</span> -</div><div class='img'><img src='loftest-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># therefore we should consider adapting the error model, although we have</span> -<span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_fit</span><span class='op'>)</span> <span class='co'># no lack of fit</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: DFOP with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 10 -40.710 -#> 2 5 -42.453 -5 3.485 0.6257</div><div class='input'><span class='co'>#</span> -<span class='co'># This is the anova model used internally for the comparison</span> -<span class='va'>test_data_anova</span> <span class='op'><-</span> <span class='va'>test_data</span> -<span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> -<span class='va'>anova_fit</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='va'>time</span>, data <span class='op'>=</span> <span class='va'>test_data_anova</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> -</div><div class='output co'>#> -#> Call: -#> lm(formula = value ~ time, data = test_data_anova) -#> -#> Residuals: -#> Min 1Q Median 3Q Max -#> -6.1000 -0.5625 0.0000 0.5625 6.1000 -#> -#> Coefficients: -#> Estimate Std. Error t value Pr(>|t|) -#> (Intercept) 103.150 2.323 44.409 7.44e-12 *** -#> time1 -19.950 3.285 -6.073 0.000185 *** -#> time3 -50.800 3.285 -15.465 8.65e-08 *** -#> time7 -68.500 3.285 -20.854 6.28e-09 *** -#> time14 -79.750 3.285 -24.278 1.63e-09 *** -#> time28 -86.000 3.285 -26.181 8.35e-10 *** -#> time60 -94.900 3.285 -28.891 3.48e-10 *** -#> time90 -98.500 3.285 -29.986 2.49e-10 *** -#> time120 -100.450 3.285 -30.580 2.09e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -#> -#> Residual standard error: 3.285 on 9 degrees of freedom -#> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 -#> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09 -#> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>anova_fit</span><span class='op'>)</span> <span class='co'># We get the same likelihood and degrees of freedom</span> -</div><div class='output co'>#> 'log Lik.' -40.71015 (df=10)</div><div class='input'><span class='co'>#</span> -<span class='va'>test_data_2</span> <span class='op'><-</span> <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_lin_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> <span class='co'># not a good model, we try parallel formation</span> -</div><div class='img'><img src='loftest-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_lin_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 7 -171.927 -21 156.64 < 2.2e-16 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='va'>m_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>sfo_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> <span class='co'># much better for metabolites</span> -</div><div class='img'><img src='loftest-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>sfo_par_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 7 -156.331 -21 125.45 < 2.2e-16 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'>#</span> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>dfop_par_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, <span class='va'>test_data_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># No visual lack of fit</span> -</div><div class='img'><img src='loftest-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'>loftest</span><span class='op'>(</span><span class='va'>dfop_par_fit</span><span class='op'>)</span> <span class='co'># no lack of fit found by the test</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: ANOVA with error model const -#> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 28 -93.606 -#> 2 9 -102.763 -19 18.313 0.5016</div><div class='input'><span class='co'>#</span> -<span class='co'># The anova model used for comparison in the case of transformation products</span> -<span class='va'>test_data_anova_2</span> <span class='op'><-</span> <span class='va'>dfop_par_fit</span><span class='op'>$</span><span class='va'>data</span> -<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>variable</span><span class='op'>)</span> -<span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/factor.html'>as.factor</a></span><span class='op'>(</span><span class='va'>test_data_anova_2</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span> -<span class='va'>anova_fit_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>observed</span> <span class='op'>~</span> <span class='va'>time</span><span class='op'>:</span><span class='va'>variable</span> <span class='op'>-</span> <span class='fl'>1</span>, data <span class='op'>=</span> <span class='va'>test_data_anova_2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>anova_fit_2</span><span class='op'>)</span> -</div><div class='output co'>#> -#> Call: -#> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2) -#> -#> Residuals: -#> Min 1Q Median 3Q Max -#> -6.1000 -0.5875 0.0000 0.5875 6.1000 -#> -#> Coefficients: (2 not defined because of singularities) -#> Estimate Std. Error t value Pr(>|t|) -#> time0:variableparent 103.150 1.573 65.562 < 2e-16 *** -#> time1:variableparent 83.200 1.573 52.882 < 2e-16 *** -#> time3:variableparent 52.350 1.573 33.274 < 2e-16 *** -#> time7:variableparent 34.650 1.573 22.024 < 2e-16 *** -#> time14:variableparent 23.400 1.573 14.873 6.35e-14 *** -#> time28:variableparent 17.150 1.573 10.901 5.47e-11 *** -#> time60:variableparent 8.250 1.573 5.244 1.99e-05 *** -#> time90:variableparent 4.650 1.573 2.956 0.006717 ** -#> time120:variableparent 2.700 1.573 1.716 0.098507 . -#> time0:variableM1 NA NA NA NA -#> time1:variableM1 11.850 1.573 7.532 6.93e-08 *** -#> time3:variableM1 22.700 1.573 14.428 1.26e-13 *** -#> time7:variableM1 33.050 1.573 21.007 < 2e-16 *** -#> time14:variableM1 31.250 1.573 19.863 < 2e-16 *** -#> time28:variableM1 18.900 1.573 12.013 7.02e-12 *** -#> time60:variableM1 7.550 1.573 4.799 6.28e-05 *** -#> time90:variableM1 3.850 1.573 2.447 0.021772 * -#> time120:variableM1 2.050 1.573 1.303 0.204454 -#> time0:variableM2 NA NA NA NA -#> time1:variableM2 6.700 1.573 4.259 0.000254 *** -#> time3:variableM2 16.750 1.573 10.646 8.93e-11 *** -#> time7:variableM2 25.800 1.573 16.399 6.89e-15 *** -#> time14:variableM2 28.600 1.573 18.178 6.35e-16 *** -#> time28:variableM2 25.400 1.573 16.144 9.85e-15 *** -#> time60:variableM2 21.600 1.573 13.729 3.81e-13 *** -#> time90:variableM2 17.800 1.573 11.314 2.51e-11 *** -#> time120:variableM2 14.100 1.573 8.962 2.79e-09 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 -#> -#> Residual standard error: 2.225 on 25 degrees of freedom -#> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 -#> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16 -#> </div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We see a clear pattern in the residuals</span></span></span> +<span class="r-plt img"><img src="loftest-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_fit</span><span class="op">)</span> <span class="co"># We have a clear lack of fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 10 -40.710 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -7 46.487 7.027e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># We try a different model (the one that was used to generate the data)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># We don't see systematic deviations, but heteroscedastic residuals</span></span></span> +<span class="r-plt img"><img src="loftest-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># therefore we should consider adapting the error model, although we have</span></span></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_fit</span><span class="op">)</span> <span class="co"># no lack of fit</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> 1 10 -40.710 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -5 3.485 0.6257</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># This is the anova model used internally for the comparison</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span> <span class="op"><-</span> <span class="va">test_data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="va">time</span>, data <span class="op">=</span> <span class="va">test_data_anova</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Call:</span> +<span class="r-out co"><span class="r-pr">#></span> lm(formula = value ~ time, data = test_data_anova)</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min 1Q Median 3Q Max </span> +<span class="r-out co"><span class="r-pr">#></span> -6.1000 -0.5625 0.0000 0.5625 6.1000 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Coefficients:</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error t value Pr(>|t|) </span> +<span class="r-out co"><span class="r-pr">#></span> (Intercept) 103.150 2.323 44.409 7.44e-12 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time1 -19.950 3.285 -6.073 0.000185 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3 -50.800 3.285 -15.465 8.65e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7 -68.500 3.285 -20.854 6.28e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14 -79.750 3.285 -24.278 1.63e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28 -86.000 3.285 -26.181 8.35e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60 -94.900 3.285 -28.891 3.48e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90 -98.500 3.285 -29.986 2.49e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time120 -100.450 3.285 -30.580 2.09e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residual standard error: 3.285 on 9 degrees of freedom</span> +<span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9953, Adjusted R-squared: 0.9912 </span> +<span class="r-out co"><span class="r-pr">#></span> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">anova_fit</span><span class="op">)</span> <span class="co"># We get the same likelihood and degrees of freedom</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 'log Lik.' -40.71015 (df=10)</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">test_data_2</span> <span class="op"><-</span> <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">sfo_lin_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span> <span class="co"># not a good model, we try parallel formation</span></span></span> +<span class="r-plt img"><img src="loftest-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_lin_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 7 -171.927 -21 156.64 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">sfo_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span> <span class="co"># much better for metabolites</span></span></span> +<span class="r-plt img"><img src="loftest-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">sfo_par_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 7 -156.331 -21 125.45 < 2.2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">dfop_par_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>, <span class="va">test_data_2</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># No visual lack of fit</span></span></span> +<span class="r-plt img"><img src="loftest-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu">loftest</span><span class="op">(</span><span class="va">dfop_par_fit</span><span class="op">)</span> <span class="co"># no lack of fit found by the test</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: ANOVA with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq)</span> +<span class="r-out co"><span class="r-pr">#></span> 1 28 -93.606 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 9 -102.763 -19 18.313 0.5016</span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The anova model used for comparison in the case of transformation products</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span> <span class="op"><-</span> <span class="va">dfop_par_fit</span><span class="op">$</span><span class="va">data</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">variable</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="va">test_data_anova_2</span><span class="op">$</span><span class="va">time</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">anova_fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">observed</span> <span class="op">~</span> <span class="va">time</span><span class="op">:</span><span class="va">variable</span> <span class="op">-</span> <span class="fl">1</span>, data <span class="op">=</span> <span class="va">test_data_anova_2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">anova_fit_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Call:</span> +<span class="r-out co"><span class="r-pr">#></span> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2)</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residuals:</span> +<span class="r-out co"><span class="r-pr">#></span> Min 1Q Median 3Q Max </span> +<span class="r-out co"><span class="r-pr">#></span> -6.1000 -0.5875 0.0000 0.5875 6.1000 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Coefficients: (2 not defined because of singularities)</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error t value Pr(>|t|) </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableparent 103.150 1.573 65.562 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableparent 83.200 1.573 52.882 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableparent 52.350 1.573 33.274 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableparent 34.650 1.573 22.024 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableparent 23.400 1.573 14.873 6.35e-14 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableparent 17.150 1.573 10.901 5.47e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableparent 8.250 1.573 5.244 1.99e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableparent 4.650 1.573 2.956 0.006717 ** </span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableparent 2.700 1.573 1.716 0.098507 . </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableM1 NA NA NA NA </span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableM1 11.850 1.573 7.532 6.93e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableM1 22.700 1.573 14.428 1.26e-13 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableM1 33.050 1.573 21.007 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableM1 31.250 1.573 19.863 < 2e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableM1 18.900 1.573 12.013 7.02e-12 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableM1 7.550 1.573 4.799 6.28e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableM1 3.850 1.573 2.447 0.021772 * </span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableM1 2.050 1.573 1.303 0.204454 </span> +<span class="r-out co"><span class="r-pr">#></span> time0:variableM2 NA NA NA NA </span> +<span class="r-out co"><span class="r-pr">#></span> time1:variableM2 6.700 1.573 4.259 0.000254 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time3:variableM2 16.750 1.573 10.646 8.93e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time7:variableM2 25.800 1.573 16.399 6.89e-15 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time14:variableM2 28.600 1.573 18.178 6.35e-16 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time28:variableM2 25.400 1.573 16.144 9.85e-15 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time60:variableM2 21.600 1.573 13.729 3.81e-13 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time90:variableM2 17.800 1.573 11.314 2.51e-11 ***</span> +<span class="r-out co"><span class="r-pr">#></span> time120:variableM2 14.100 1.573 8.962 2.79e-09 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Residual standard error: 2.225 on 25 degrees of freedom</span> +<span class="r-out co"><span class="r-pr">#></span> Multiple R-squared: 0.9979, Adjusted R-squared: 0.9957 </span> +<span class="r-out co"><span class="r-pr">#></span> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index 3e9452c6..e77121d1 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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<pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>An object of class <code><a href='https://rdrr.io/r/stats/logLik.html'>logLik</a></code> with the number of estimated + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - + </div> + <div id="details"> + <h2>Details</h2> <p>The total number of estimated parameters returned with the value of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - - <div class='dont-index'><p>Compare the AIC of columns of <code><a href='mmkin.html'>mmkin</a></code> objects using -<code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p>Compare the AIC of columns of <code><a href="mmkin.html">mmkin</a></code> objects using +<code><a href="AIC.mmkin.html">AIC.mmkin</a></code>.</p></div> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># \dontrun{</span> - <span class='va'>sfo_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span> - <span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>d_t</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> - <span class='va'>f_nw</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>sfo_sfo</span>, <span class='va'>d_t</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='co'># no weighting (weights are unity)</span> - <span class='va'>f_obs</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> - <span class='va'>f_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nw</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nw</span>, <span class='va'>f_obs</span>, <span class='va'>f_tc</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> f_nw 5 204.4486 -#> f_obs 6 205.8727 -#> f_tc 6 141.9656</div><div class='input'> <span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">d_t</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_nw</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">sfo_sfo</span>, <span class="va">d_t</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span> <span class="co"># no weighting (weights are unity)</span></span></span> +<span class="r-in"><span> <span class="va">f_obs</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"obs"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_nw</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nw</span>, <span class="va">f_obs</span>, <span class="va">f_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_nw 5 204.4486</span> +<span class="r-out co"><span class="r-pr">#></span> f_obs 6 205.8727</span> +<span class="r-out co"><span class="r-pr">#></span> f_tc 6 141.9656</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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<span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html index 1d1880fd..ac4961bc 100644 --- a/docs/dev/reference/logistic.solution.html +++ b/docs/dev/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><meta name=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ an increasing rate constant, supposedly caused by microbial growth"><meta name=" <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html index f2d8472e..a7198474 100644 --- a/docs/dev/reference/lrtest.mkinfit.html +++ b/docs/dev/reference/lrtest.mkinfit.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - 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If two fitted +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Likelihood ratio test for mkinfit models — lrtest.mkinfit"><meta property="og:description" content="Compare two mkinfit models based on their likelihood. If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom -and can be expressed by fixing the parameters of the other." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +and can be expressed by fixing the parameters of the other."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ and can be expressed by fixing the parameters of the other." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,48 +45,50 @@ and can be expressed by fixing the parameters of the other." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Likelihood ratio test for mkinfit models</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/lrtest.mkinfit.R'><code>R/lrtest.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a></small> <div class="hidden name"><code>lrtest.mkinfit.Rd</code></div> </div> @@ -155,115 +100,117 @@ that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, object_2 <span class='op'>=</span> <span class='cn'>NULL</span>, <span class='va'>...</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object, or an <code><a href="mmkin.html">mmkin</a></code> column +object containing two fits to the same data.</p></dd> + -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> +<dt>object_2</dt> +<dd><p>Optionally, another mkinfit object fitted to the same data.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object, or an <code><a href='mmkin.html'>mmkin</a></code> column -object containing two fits to the same data.</p></td> - </tr> - <tr> - <th>object_2</th> - <td><p>Optionally, another mkinfit object fitted to the same data.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Argument to <code><a href='mkinfit.html'>mkinfit</a></code>, passed to -<code><a href='update.mkinfit.html'>update.mkinfit</a></code> for creating the alternative fitted object.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +<dt>...</dt> +<dd><p>Argument to <code><a href="mkinfit.html">mkinfit</a></code>, passed to +<code><a href="update.mkinfit.html">update.mkinfit</a></code> for creating the alternative fitted object.</p></dd> +</dl></div> + <div id="details"> + <h2>Details</h2> <p>Alternatively, an argument to mkinfit can be given which is then passed -to <code><a href='update.mkinfit.html'>update.mkinfit</a></code> to obtain the alternative model.</p> -<p>The comparison is then made by the <code><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest.default</a></code> +to <code><a href="update.mkinfit.html">update.mkinfit</a></code> to obtain the alternative model.</p> +<p>The comparison is then made by the <code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> method from the lmtest package. The model with the higher number of fitted parameters (alternative hypothesis) is listed first, then the model with the lower number of fitted parameters (null hypothesis).</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>test_data</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>12</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, <span class='va'>name</span> <span class='op'>==</span> <span class='st'>"parent"</span><span class='op'>)</span> -<span class='va'>sfo_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>dfop_fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>test_data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='va'>sfo_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 3 -63.954 -2 43.002 4.594e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>sfo_fit</span>, <span class='va'>dfop_fit</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: SFO with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 3 -63.954 -2 43.002 4.594e-10 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'> -<span class='co'># The following two examples are commented out as they fail during</span> -<span class='co'># generation of the static help pages by pkgdown</span> -<span class='co'>#lrtest(dfop_fit, error_model = "tc")</span> -<span class='co'>#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span> - -<span class='co'># However, this equivalent syntax also works for static help pages</span> -<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model tc -#> Model 2: DFOP with error model const -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 6 -34.587 -#> 2 5 -42.453 -1 15.731 7.302e-05 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>dfop_fit</span>, fixed_parms <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> Likelihood ratio test -#> -#> Model 1: DFOP with error model const -#> Model 2: DFOP with error model const and fixed parameter(s) k2 -#> #Df LogLik Df Chisq Pr(>Chisq) -#> 1 5 -42.453 -#> 2 4 -57.340 -1 29.776 4.851e-08 *** -#> --- -#> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">dfop_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="va">sfo_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">sfo_fit</span>, <span class="va">dfop_fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: SFO with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 3 -63.954 -2 43.002 4.594e-10 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following two examples are commented out as they fail during</span></span></span> +<span class="r-in"><span><span class="co"># generation of the static help pages by pkgdown</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, error_model = "tc")</span></span></span> +<span class="r-in"><span><span class="co">#lrtest(dfop_fit, fixed_parms = c(k2 = 0))</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># However, this equivalent syntax also works for static help pages</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model tc</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 6 -34.587 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 5 -42.453 -1 15.731 7.302e-05 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">dfop_fit</span>, <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_fit</span>, fixed_parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Likelihood ratio test</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model 1: DFOP with error model const</span> +<span class="r-out co"><span class="r-pr">#></span> Model 2: DFOP with error model const and fixed parameter(s) k2</span> +<span class="r-out co"><span class="r-pr">#></span> #Df LogLik Df Chisq Pr(>Chisq) </span> +<span class="r-out co"><span class="r-pr">#></span> 1 5 -42.453 </span> +<span class="r-out co"><span class="r-pr">#></span> 2 4 -57.340 -1 29.776 4.851e-08 ***</span> +<span class="r-out co"><span class="r-pr">#></span> ---</span> +<span class="r-out co"><span class="r-pr">#></span> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div 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Currently, only calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models, using the analytical formulas given in the PEC -soil section of the FOCUS guidance." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +soil section of the FOCUS guidance."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - 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<ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -104,171 +47,176 @@ soil section of the FOCUS guidance." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/max_twa_parent.R'><code>R/max_twa_parent.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/max_twa_parent.R" class="external-link"><code>R/max_twa_parent.R</code></a></small> <div class="hidden name"><code>max_twa_parent.Rd</code></div> </div> <div class="ref-description"> <p>This function calculates maximum moving window time weighted average -concentrations (TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. +concentrations (TWAs) for kinetic models fitted with <code><a href="mkinfit.html">mkinfit</a></code>. Currently, only calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.</p> </div> - <pre class="usage"><span class='fu'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>windows</span><span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="va">windows</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_sfo</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_fomc</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">alpha</span>, <span class="va">beta</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_dfop</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">t</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">max_twa_hs</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span>, <span class="va">t</span><span class="op">)</span></span></code></pre></div> + </div> -<span class='fu'>max_twa_sfo</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k</span>, <span class='va'>t</span><span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> -<span class='fu'>max_twa_fomc</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>alpha</span>, <span class='va'>beta</span>, <span class='va'>t</span><span class='op'>)</span> -<span class='fu'>max_twa_dfop</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>g</span>, <span class='va'>t</span><span class='op'>)</span> +<dt>windows</dt> +<dd><p>The width of the time windows for which the TWAs should be +calculated.</p></dd> -<span class='fu'>max_twa_hs</span><span class='op'>(</span>M0 <span class='op'>=</span> <span class='fl'>1</span>, <span class='va'>k1</span>, <span class='va'>k2</span>, <span class='va'>tb</span>, <span class='va'>t</span><span class='op'>)</span></pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>An object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>windows</th> - <td><p>The width of the time windows for which the TWAs should be -calculated.</p></td> - </tr> - <tr> - <th>M0</th> - <td><p>The initial concentration for which the maximum time weighted +<dt>M0</dt> +<dd><p>The initial concentration for which the maximum time weighted average over the decline curve should be calculated. The default is to use a value of 1, which means that a relative maximum time weighted average -factor (f_twa) is calculated.</p></td> - </tr> - <tr> - <th>k</th> - <td><p>The rate constant in the case of SFO kinetics.</p></td> - </tr> - <tr> - <th>t</th> - <td><p>The width of the time window.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>Parameter of the FOMC model.</p></td> - </tr> - <tr> - <th>beta</th> - <td><p>Parameter of the FOMC model.</p></td> - </tr> - <tr> - <th>k1</th> - <td><p>The first rate constant of the DFOP or the HS kinetics.</p></td> - </tr> - <tr> - <th>k2</th> - <td><p>The second rate constant of the DFOP or the HS kinetics.</p></td> - </tr> - <tr> - <th>g</th> - <td><p>Parameter of the DFOP model.</p></td> - </tr> - <tr> - <th>tb</th> - <td><p>Parameter of the HS model.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>For <code>max_twa_parent</code>, a numeric vector, named using the +factor (f_twa) is calculated.</p></dd> + + +<dt>k</dt> +<dd><p>The rate constant in the case of SFO kinetics.</p></dd> + + +<dt>t</dt> +<dd><p>The width of the time window.</p></dd> + + +<dt>alpha</dt> +<dd><p>Parameter of the FOMC model.</p></dd> + + +<dt>beta</dt> +<dd><p>Parameter of the FOMC model.</p></dd> + + +<dt>k1</dt> +<dd><p>The first rate constant of the DFOP or the HS kinetics.</p></dd> + + +<dt>k2</dt> +<dd><p>The second rate constant of the DFOP or the HS kinetics.</p></dd> + + +<dt>g</dt> +<dd><p>Parameter of the DFOP model.</p></dd> + + +<dt>tb</dt> +<dd><p>Parameter of the HS model.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>For <code>max_twa_parent</code>, a numeric vector, named using the <code>windows</code> argument. For the other functions, a numeric vector of length one (also known as 'a number').</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in -EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, +EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'>max_twa_parent</span><span class='op'>(</span><span class='va'>fit</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>7</span>, <span class='fl'>21</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> 7 21 -#> 34.71343 18.22124 </div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> 7 21 </span> +<span class="r-out co"><span class="r-pr">#></span> 34.71343 18.22124 </span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,44 +43,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</h1> @@ -151,120 +96,135 @@ extracts.</p> </div> - <pre class="usage"><span class='va'>mccall81_245T</span></pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div> + </div> - <p>A dataframe containing the following variables.</p><dl> - <dt><code>name</code></dt><dd><p>the name of the compound observed. Note that T245 is used as + <div id="format"> + <h2>Format</h2> + <p>A dataframe containing the following variables.</p><dl><dt><code>name</code></dt> +<dd><p>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name in R, which is necessary for specifying models using - <code><a href='mkinmod.html'>mkinmod</a></code>.</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing sampling times in days after + <code><a href="mkinmod.html">mkinmod</a></code>.</p></dd> + + <dt><code>time</code></dt> +<dd><p>a numeric vector containing sampling times in days after treatment</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> - <dt><code>soil</code></dt><dd><p>a factor containing the name of the soil</p></dd> - -</dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <dt><code>value</code></dt> +<dd><p>a numeric vector containing concentrations in percent of applied radioactivity</p></dd> + + <dt><code>soil</code></dt> +<dd><p>a factor containing the name of the soil</p></dd> + +</dl></div> + <div id="source"> + <h2>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 - doi: <a href='https://doi.org/10.1021/jf00103a026'>10.1021/jf00103a026</a></p> + <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='va'>SFO_SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span> - <span class='va'>fit.1</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) -#> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18 -#> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 -#> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02 -#> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 -#> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02 -#> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02 -#> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05 -#> Lower Upper -#> T245_0 99.246061385 1.084640e+02 -#> k_T245 0.039631621 4.746194e-02 -#> k_phenol 0.218013879 7.525762e-01 -#> k_anisole 0.005370739 8.305299e-03 -#> f_T245_to_phenol 0.547559081 6.924813e-01 -#> f_phenol_to_anisole 0.000000000 1.000000e+00 -#> sigma 1.706607296 3.322649e+00</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 -#> -#> $distimes -#> DT50 DT90 -#> T245 15.982025 53.09114 -#> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 -#> </div><div class='input'> <span class='co'># formation fraction from phenol to anisol is practically 1. As we cannot</span> - <span class='co'># fix formation fractions when using the ilr transformation, we can turn of</span> - <span class='co'># the sink in the model generation</span> - <span class='va'>SFO_SFO_SFO_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>T245 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"phenol"</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"anisole"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO_SFO_2</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284 -#> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 -#> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587 -#> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 -#> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637 -#> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 -#> Upper -#> T245_0 108.43904074 -#> k_T245 0.04743877 -#> k_phenol 0.75005585 -#> k_anisole 0.00829550 -#> f_T245_to_phenol 0.69212308 -#> sigma 3.31827222</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.1</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> T245_phenol T245_sink phenol_anisole phenol_sink -#> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 -#> -#> $distimes -#> DT50 DT90 -#> T245 15.982025 53.09114 -#> phenol 1.711229 5.68458 -#> anisole 103.784093 344.76329 -#> </div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -</div><div class='img'><img src='mccall81_245T-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit.1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t)</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1847074945 47.537272 4.472189e-18</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050581e-01 0.2986993563 1.356073 9.756989e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.3985340558 1.562627 6.949413e-02</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 1.000000e+00 0.6718439825 1.488441 7.867789e-02</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.4907558883 5.123989 6.233157e-05</span> +<span class="r-out co"><span class="r-pr">#></span> Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 99.246061385 1.084640e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.039631621 4.746194e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.218013879 7.525762e-01</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.005370739 8.305299e-03</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.547559081 6.924813e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_phenol_to_anisole 0.000000000 1.000000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.706607296 3.322649e+00</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># formation fraction from phenol to anisol is practically 1. As we cannot</span></span></span> +<span class="r-in"><span> <span class="co"># fix formation fractions when using the ilr transformation, we can turn of</span></span></span> +<span class="r-in"><span> <span class="co"># the sink in the model generation</span></span></span> +<span class="r-in"><span> <span class="va">SFO_SFO_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO_SFO_2</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 1.038550e+02 2.1623653066 48.028439 4.993108e-19 99.271020284</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 4.050582e-01 0.1177237473 3.440752 1.679254e-03 0.218746587</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 6.227599e-01 0.0342197875 18.198824 2.039411e-12 0.547975637</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> T245_0 108.43904074</span> +<span class="r-out co"><span class="r-pr">#></span> k_T245 0.04743877</span> +<span class="r-out co"><span class="r-pr">#></span> k_phenol 0.75005585</span> +<span class="r-out co"><span class="r-pr">#></span> k_anisole 0.00829550</span> +<span class="r-out co"><span class="r-pr">#></span> f_T245_to_phenol 0.69212308</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.31827222</span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit.1</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> T245_phenol T245_sink phenol_anisole phenol_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 6.227599e-01 3.772401e-01 1.000000e+00 3.773626e-10 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> T245 15.982025 53.09114</span> +<span class="r-out co"><span class="r-pr">#></span> phenol 1.711229 5.68458</span> +<span class="r-out co"><span class="r-pr">#></span> anisole 103.784093 344.76329</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mccall81_245T-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mean_degparms.html b/docs/dev/reference/mean_degparms.html index 67db1868..feb37a1d 100644 --- a/docs/dev/reference/mean_degparms.html +++ b/docs/dev/reference/mean_degparms.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -44,19 +44,25 @@ <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html index e87e20a1..e72d17f9 100644 --- a/docs/dev/reference/mhmkin.html +++ b/docs/dev/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -64,7 +64,10 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mixed-1.png b/docs/dev/reference/mixed-1.png Binary files differindex 54b81b70..dbba1b03 100644 --- a/docs/dev/reference/mixed-1.png +++ b/docs/dev/reference/mixed-1.png diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html index b2b83312..01a0614b 100644 --- a/docs/dev/reference/mixed.html +++ b/docs/dev/reference/mixed.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -26,7 +26,7 @@ <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -41,19 +41,28 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -84,73 +93,84 @@ </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mmkin</span> -<span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span> - -<span class="co"># S3 method for mixed.mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"none"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mixed.mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object</p></dd> + + <dt>...</dt> <dd><p>Currently not used</p></dd> + + <dt>method</dt> <dd><p>The method to be used</p></dd> + + <dt>x</dt> <dd><p>A mixed.mmkin object to print</p></dd> + + <dt>digits</dt> <dd><p>Number of digits to use for printing.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>An object of class 'mixed.mmkin' which has the observed data in a + + +<p>An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting</p> </div> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span> -<span class="r-in"><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span> -<span class="r-in"> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span> -<span class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span> -<span class="r-in"> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span> -<span class="r-in"><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span> -<span class="r-in"><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> -<span class="r-in"> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span> -<span class="r-in"> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span> -<span class="r-in"> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span> -<span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"> <span class="op">}</span></span> -<span class="r-in"><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span> -<span class="r-in"> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span> -<span class="r-in"> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span> -<span class="r-in"> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span> -<span class="r-in"><span class="op">}</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="co"># \dontrun{</span></span> -<span class="r-in"><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span></span> +<span class="r-in"><span><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">DFOP_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">log_sd</span> <span class="op"><-</span> <span class="fl">0.3</span></span></span> +<span class="r-in"><span><span class="va">syn_biphasic_parms</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">as.matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> k1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.05</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.01</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> g <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> f_parent_to_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fl">0</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> k_m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="va">n_biphasic</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.002</span><span class="op">)</span>, <span class="va">log_sd</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic_mean</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="va">n_biphasic</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">syn_biphasic_parms</span><span class="op">[</span><span class="va">i</span>, <span class="op">]</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456L</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds_biphasic</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_biphasic_mean</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span></span> +<span class="r-in"><span> sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">err_1</span><span class="op">$</span><span class="va">const</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">err_1</span><span class="op">$</span><span class="va">prop</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> n <span class="op">=</span> <span class="fl">1</span>, secondary <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="op">}</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">f_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"DFOP-SFO"</span> <span class="op">=</span> <span class="va">DFOP_SFO</span><span class="op">)</span>, <span class="va">ds_biphasic</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f_mixed</span> <span class="op"><-</span> <span class="fu">mixed</span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Kinetic model fitted by nonlinear regression to each dataset</span> <span class="r-out co"><span class="r-pr">#></span> Structural model:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -177,9 +197,9 @@ single dataframe which is convenient for plotting</p> <span class="r-out co"><span class="r-pr">#></span> 100.674757 -8.761916 -0.004347 -3.348812 -3.986853 </span> <span class="r-out co"><span class="r-pr">#></span> g_qlogis </span> <span class="r-out co"><span class="r-pr">#></span> -0.087392 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_mixed</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="mixed-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># }</span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> </div> @@ -194,7 +214,7 @@ single dataframe which is convenient for plotting</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html index 6246fbe2..3e55885f 100644 --- a/docs/dev/reference/mkin_long_to_wide.html +++ b/docs/dev/reference/mkin_long_to_wide.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" /> -<meta property="og:description" content="This function takes a dataframe in the long form, i.e. with a row for each +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Convert a dataframe from long to wide format — mkin_long_to_wide • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide"><meta property="og:description" content="This function takes a dataframe in the long form, i.e. with a row for each observed value, and converts it into a dataframe with one independent -variable and several dependent variables as columns." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +variable and several dependent variables as columns."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ variable and several dependent variables as columns." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,48 +43,50 @@ variable and several dependent variables as columns." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe from long to wide format</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_long_to_wide.R'><code>R/mkin_long_to_wide.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_long_to_wide.R" class="external-link"><code>R/mkin_long_to_wide.R</code></a></small> <div class="hidden name"><code>mkin_long_to_wide.Rd</code></div> </div> @@ -151,87 +96,89 @@ observed value, and converts it into a dataframe with one independent variable and several dependent variables as columns.</p> </div> - <pre class="usage"><span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>long_data</span>, time <span class='op'>=</span> <span class='st'>"time"</span>, outtime <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">long_data</span>, time <span class="op">=</span> <span class="st">"time"</span>, outtime <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>long_data</th> - <td><p>The dataframe must contain one variable called "time" with + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>long_data</dt> +<dd><p>The dataframe must contain one variable called "time" with the time values specified by the <code>time</code> argument, one column called "name" with the grouping of the observed values, and finally one column of -observed values called "value".</p></td> - </tr> - <tr> - <th>time</th> - <td><p>The name of the time variable in the long input data.</p></td> - </tr> - <tr> - <th>outtime</th> - <td><p>The name of the time variable in the wide output data.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Dataframe in wide format.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +observed values called "value".</p></dd> + + +<dt>time</dt> +<dd><p>The name of the time variable in the long input data.</p></dd> + + +<dt>outtime</dt> +<dd><p>The name of the time variable in the wide output data.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>Dataframe in wide format.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='fu'>mkin_long_to_wide</span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span><span class='op'>)</span> -</div><div class='output co'>#> time parent m1 -#> 1 0 99.46 0.00 -#> 2 0 102.04 0.00 -#> 3 1 93.50 4.84 -#> 4 1 92.50 5.64 -#> 5 3 63.23 12.91 -#> 6 3 68.99 12.96 -#> 7 7 52.32 22.97 -#> 8 7 55.13 24.47 -#> 9 14 27.27 41.69 -#> 10 14 26.64 33.21 -#> 11 21 11.50 44.37 -#> 12 21 11.64 46.44 -#> 13 35 2.85 41.22 -#> 14 35 2.91 37.95 -#> 15 50 0.69 41.19 -#> 16 50 0.63 40.01 -#> 17 75 0.05 40.09 -#> 18 75 0.06 33.85 -#> 19 100 NA 31.04 -#> 20 100 NA 33.13 -#> 21 120 NA 25.15 -#> 22 120 NA 33.31</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> time parent m1</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0 99.46 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0 102.04 0.00</span> +<span class="r-out co"><span class="r-pr">#></span> 3 1 93.50 4.84</span> +<span class="r-out co"><span class="r-pr">#></span> 4 1 92.50 5.64</span> +<span class="r-out co"><span class="r-pr">#></span> 5 3 63.23 12.91</span> +<span class="r-out co"><span class="r-pr">#></span> 6 3 68.99 12.96</span> +<span class="r-out co"><span class="r-pr">#></span> 7 7 52.32 22.97</span> +<span class="r-out co"><span class="r-pr">#></span> 8 7 55.13 24.47</span> +<span class="r-out co"><span class="r-pr">#></span> 9 14 27.27 41.69</span> +<span class="r-out co"><span class="r-pr">#></span> 10 14 26.64 33.21</span> +<span class="r-out co"><span class="r-pr">#></span> 11 21 11.50 44.37</span> +<span class="r-out co"><span class="r-pr">#></span> 12 21 11.64 46.44</span> +<span class="r-out co"><span class="r-pr">#></span> 13 35 2.85 41.22</span> +<span class="r-out co"><span class="r-pr">#></span> 14 35 2.91 37.95</span> +<span class="r-out co"><span class="r-pr">#></span> 15 50 0.69 41.19</span> +<span class="r-out co"><span class="r-pr">#></span> 16 50 0.63 40.01</span> +<span class="r-out co"><span class="r-pr">#></span> 17 75 0.05 40.09</span> +<span class="r-out co"><span class="r-pr">#></span> 18 75 0.06 33.85</span> +<span class="r-out co"><span class="r-pr">#></span> 19 100 NA 31.04</span> +<span class="r-out co"><span class="r-pr">#></span> 20 100 NA 33.13</span> +<span class="r-out co"><span class="r-pr">#></span> 21 120 NA 25.15</span> +<span class="r-out co"><span class="r-pr">#></span> 22 120 NA 33.31</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkin_wide_to_long.html 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property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long"><meta property="og:description" content="This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by -mkinfit." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" 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class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,118 +43,122 @@ mkinfit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Convert a dataframe with observations over time into long format</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkin_wide_to_long.R'><code>R/mkin_wide_to_long.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_wide_to_long.R" class="external-link"><code>R/mkin_wide_to_long.R</code></a></small> <div class="hidden name"><code>mkin_wide_to_long.Rd</code></div> </div> <div class="ref-description"> <p>This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by -<code><a href='mkinfit.html'>mkinfit</a></code>.</p> +<code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide_data</span>, time <span class='op'>=</span> <span class='st'>"t"</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide_data</span>, time <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>wide_data</th> - <td><p>The dataframe must contain one variable with the time + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>wide_data</dt> +<dd><p>The dataframe must contain one variable with the time values specified by the <code>time</code> argument and usually more than one -column of observed values.</p></td> - </tr> - <tr> - <th>time</th> - <td><p>The name of the time variable.</p></td> - </tr> - </table> +column of observed values.</p></dd> + - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>time</dt> +<dd><p>The name of the time variable.</p></dd> - <p>Dataframe in long format as needed for <code><a href='mkinfit.html'>mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>Dataframe in long format as needed for <code><a href="mkinfit.html">mkinfit</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>wide</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>t <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span><span class='op'>)</span>, x <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span><span class='op'>)</span>, y <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'>mkin_wide_to_long</span><span class='op'>(</span><span class='va'>wide</span><span class='op'>)</span> -</div><div class='output co'>#> name time value -#> 1 x 1 1 -#> 2 x 2 4 -#> 3 x 3 7 -#> 4 y 1 3 -#> 5 y 2 4 -#> 6 y 3 5</div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">3</span><span class="op">)</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">4</span>,<span class="fl">7</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> name time value</span> +<span class="r-out co"><span class="r-pr">#></span> 1 x 1 1</span> +<span class="r-out co"><span class="r-pr">#></span> 2 x 2 4</span> +<span class="r-out co"><span class="r-pr">#></span> 3 x 3 7</span> +<span class="r-out co"><span class="r-pr">#></span> 4 y 1 3</span> +<span class="r-out co"><span class="r-pr">#></span> 5 y 2 4</span> +<span class="r-out co"><span class="r-pr">#></span> 6 y 3 5</span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinds.html b/docs/dev/reference/mkinds.html index b571e3a0..a7fb9916 100644 --- a/docs/dev/reference/mkinds.html +++ b/docs/dev/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -47,19 +47,25 @@ provided by this package come as mkinds objects nevertheless."><meta name="robot <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html index d19a7a1d..cbf55fca 100644 --- a/docs/dev/reference/mkindsg.html +++ b/docs/dev/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><meta name="robots" content="noindex"><!-- mat </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -47,19 +47,25 @@ dataset if no data are supplied."><meta name="robots" content="noindex"><!-- mat <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html index 94c575cb..2c9f0b13 100644 --- a/docs/dev/reference/mkinerrmin.html +++ b/docs/dev/reference/mkinerrmin.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" 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resulting in passing +the chi-squared test as defined in the FOCUS kinetics report from 2006."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculate the minimum error to assume in order to pass the variance test</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrmin.R'><code>R/mkinerrmin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrmin.R" class="external-link"><code>R/mkinerrmin.R</code></a></small> <div class="hidden name"><code>mkinerrmin.Rd</code></div> </div> @@ -149,89 +94,100 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006." /> the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </div> - <pre class="usage"><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit</span>, alpha <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The confidence level chosen for the chi-squared test.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>A dataframe with the following components:</p> -<dt>err.min</dt><dd><p>The -relative error, expressed as a fraction.</p></dd> <dt>n.optim</dt><dd><p>The number of -optimised parameters attributed to the data series.</p></dd> <dt>df</dt><dd><p>The number of + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> + + +<dt>alpha</dt> +<dd><p>The confidence level chosen for the chi-squared test.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A dataframe with the following components:</p> +<dl><dt>err.min</dt> +<dd><p>The +relative error, expressed as a fraction.</p></dd> + <dt>n.optim</dt> +<dd><p>The number of +optimised parameters attributed to the data series.</p></dd> + <dt>df</dt> +<dd><p>The number of remaining degrees of freedom for the chi2 error level calculations. Note that mean values are used for the chi2 statistic and therefore every time -point with observed values in the series only counts one time.</p></dd> The +point with observed values in the series only counts one time.</p></dd> +</dl><p>The dataframe has one row for the total dataset and one further row for each -observed state variable in the model. - - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>This function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - - <p>FOCUS (2006) “Guidance Document on Estimating Persistence +observed state variable in the model.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>This function is used internally by <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>.</p> + </div> + <div id="references"> + <h2>References</h2> + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU -Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC +Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, -<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO_SFO</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit_FOCUS_D</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_D</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.0640 4 15 -#> parent 0.0646 2 7 -#> m1 0.0469 2 8</div><div class='input'><span class='co'># \dontrun{</span> - <span class='va'>fit_FOCUS_E</span> <span class='op'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_2006_E</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span><span class='op'>(</span><span class='fu'>mkinerrmin</span><span class='op'>(</span><span class='va'>fit_FOCUS_E</span><span class='op'>)</span>, <span class='fl'>4</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.1544 4 13 -#> parent 0.1659 2 7 -#> m1 0.1095 2 6</div><div class='input'><span class='co'># }</span> - -</div></pre> +<a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit_FOCUS_D</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_D</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.0640 4 15</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.0646 2 7</span> +<span class="r-out co"><span class="r-pr">#></span> m1 0.0469 2 8</span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit_FOCUS_E</span> <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_2006_E</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/Round.html" class="external-link">round</a></span><span class="op">(</span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit_FOCUS_E</span><span class="op">)</span>, <span class="fl">4</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.1544 4 13</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.1659 2 7</span> +<span class="r-out co"><span class="r-pr">#></span> m1 0.1095 2 6</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinerrplot-1.png b/docs/dev/reference/mkinerrplot-1.png Binary files differindex bae6071d..49bb1c0e 100644 --- a/docs/dev/reference/mkinerrplot-1.png +++ b/docs/dev/reference/mkinerrplot-1.png diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html index 7f1fd048..66bfb508 100644 --- a/docs/dev/reference/mkinerrplot.html +++ b/docs/dev/reference/mkinerrplot.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model and this error model plot can be obtained with plot.mkinfit -using the argument show_errplot = TRUE." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +using the argument show_errplot = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ using the argument show_errplot = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,48 +45,50 @@ using the argument show_errplot = TRUE." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot squared residuals and the error model for an mkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrplot.R" class="external-link"><code>R/mkinerrplot.R</code></a></small> <div class="hidden name"><code>mkinerrplot.Rd</code></div> </div> @@ -151,128 +96,133 @@ using the argument show_errplot = TRUE." /> <p>This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model -and this error model plot can be obtained with <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> +and this error model plot can be obtained with <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the argument <code>show_errplot = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinerrplot</span><span class='op'>(</span> - <span class='va'>object</span>, - obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, - xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>predicted</span><span class='op'>)</span><span class='op'>)</span>, - xlab <span class='op'>=</span> <span class='st'>"Predicted"</span>, - ylab <span class='op'>=</span> <span class='st'>"Squared residual"</span>, - maxy <span class='op'>=</span> <span class='st'>"auto"</span>, - legend <span class='op'>=</span> <span class='cn'>TRUE</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - <tr> - <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">predicted</span><span class="op">)</span><span class="op">)</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Predicted"</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Squared residual"</span>,</span> +<span> maxy <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + +<dt>obs_vars</dt> +<dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in -the model</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>plot range in x direction.</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>maxy</th> - <td><p>Maximum value of the residuals. This is used for the scaling of -the y axis and defaults to "auto".</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be plotted?</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Where should the legend be placed? Default is "topright". Will -be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> - </tr> - <tr> - <th>col_obs</th> - <td><p>Colors for the observed variables.</p></td> - </tr> - <tr> - <th>pch_obs</th> - <td><p>Symbols to be used for the observed variables.</p></td> - </tr> - <tr> - <th>frame</th> - <td><p>Should a frame be drawn around the plots?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side -effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +the model</p></dd> - <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted -lines of the mkinfit object.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> +<dt>xlim</dt> +<dd><p>plot range in x direction.</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>maxy</dt> +<dd><p>Maximum value of the residuals. This is used for the scaling of +the y axis and defaults to "auto".</p></dd> + + +<dt>legend</dt> +<dd><p>Should a legend be plotted?</p></dd> + + +<dt>lpos</dt> +<dd><p>Where should the legend be placed? Default is "topright". Will +be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinerrplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='mkinerrplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +<dt>col_obs</dt> +<dd><p>Colors for the observed variables.</p></dd> -</div></pre> + +<dt>pch_obs</dt> +<dd><p>Symbols to be used for the observed variables.</p></dd> + + +<dt>frame</dt> +<dd><p>Should a frame be drawn around the plots?</p></dd> + + +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>Nothing is returned by this function, as it is called for its side +effect, namely to produce a plot.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted +lines of the mkinfit object.</p></div> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu">mkinerrplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinerrplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 17da44cb..ee596e89 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -67,7 +67,10 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -381,17 +384,17 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:26 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:26 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:05:53 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:05:53 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.049 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.045 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> @@ -531,11 +534,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> analytical <span class="op">=</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.559</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.556 0.870</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.603 1.455</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.616</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.505 0.927</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.455 1.512</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -562,10 +564,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:09:37 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:09:37 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:06:05 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:06:05 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -574,7 +576,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.43 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 2.81 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index d0e192e7..251215a7 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -310,7 +310,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span>, full_name <span class="op">=</span> <span class="st">"Test compound"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmpp1dECS/file32009e039f7a.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpbZbZ8Y/file8c6a9f402f42.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -363,7 +363,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55555d516c10></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55556029f678></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/dev/reference/mkinparplot-1.png b/docs/dev/reference/mkinparplot-1.png Binary files differindex c9ed49eb..fff98391 100644 --- a/docs/dev/reference/mkinparplot-1.png +++ b/docs/dev/reference/mkinparplot-1.png diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html index bac6e71c..99b0ab33 100644 --- a/docs/dev/reference/mkinparplot.html +++ b/docs/dev/reference/mkinparplot.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,112 +42,119 @@ mkinfit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot the confidence intervals obtained using mkinfit</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinparplot.R'><code>R/mkinparplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinparplot.R" class="external-link"><code>R/mkinparplot.R</code></a></small> <div class="hidden name"><code>mkinparplot.Rd</code></div> </div> <div class="ref-description"> <p>This function plots the confidence intervals for the parameters fitted using -<code><a href='mkinfit.html'>mkinfit</a></code>.</p> +<code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <pre class="usage"><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - </table> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + - <p>Nothing is returned by this function, as it is called for its side +<p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - T245 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"phenol"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - phenol <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"anisole"</span><span class='op'>)</span><span class='op'>)</span>, - anisole <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>mccall81_245T</span>, <span class='va'>soil</span> <span class='op'>==</span> <span class='st'>"Commerce"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>false convergence (8)</span></div><div class='input'><span class='fu'>mkinparplot</span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> T245 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"phenol"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"anisole"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">mccall81_245T</span>, <span class="va">soil</span> <span class="op">==</span> <span class="st">"Commerce"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> +<span class="r-in"><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinparplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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It now only calls the plot method +plot.mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ plot.mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,103 +42,104 @@ plot.mkinfit." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the observed data and the fitted model of an mkinfit object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mkinfit.R'><code>R/plot.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small> <div class="hidden name"><code>mkinplot.Rd</code></div> </div> <div class="ref-description"> <p>Deprecated function. It now only calls the plot method -<code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p> +<code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinplot</span><span class="op">(</span><span class="va">fit</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>mkinplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>fit</dt> +<dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>fit</th> - <td><p>an object of class <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>The function is called for its side effect.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 0e645b51..10d2c9a9 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -372,11 +372,10 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> <span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.2 0.021</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.2 0.021</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.4 0.022</span> <span class="r-out co"><span class="r-pr">#></span> 3 deSolve 41.0 0.205</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> diff --git a/docs/dev/reference/mkinresplot-1.png b/docs/dev/reference/mkinresplot-1.png Binary files differindex ffd34f6f..97ccd762 100644 --- a/docs/dev/reference/mkinresplot-1.png +++ b/docs/dev/reference/mkinresplot-1.png diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html index 30377f2c..4d99f5be 100644 --- a/docs/dev/reference/mkinresplot.html +++ b/docs/dev/reference/mkinresplot.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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-<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> -<meta property="og:description" content="This function plots the residuals for the specified subset of the observed +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function to plot residuals stored in an mkin object — mkinresplot • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot"><meta property="og:description" content="This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted model and the residuals can be obtained using plot.mkinfit using the -argument show_residuals = TRUE." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +argument show_residuals = TRUE."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ argument show_residuals = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,181 +44,188 @@ argument show_residuals = TRUE." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Function to plot residuals stored in an mkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinresplot.R" class="external-link"><code>R/mkinresplot.R</code></a></small> <div class="hidden name"><code>mkinresplot.Rd</code></div> </div> <div class="ref-description"> <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted model and -the residuals can be obtained using <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> using the +the residuals can be obtained using <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> </div> - <pre class="usage"><span class='fu'>mkinresplot</span><span class='op'>(</span> - <span class='va'>object</span>, - obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, - xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1.1</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Extremes.html'>max</a></span><span class='op'>(</span><span class='va'>object</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span><span class='op'>)</span>, - standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, - xlab <span class='op'>=</span> <span class='st'>"Time"</span>, - ylab <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='va'>standardized</span>, <span class='st'>"Standardized residual"</span>, <span class='st'>"Residual"</span><span class='op'>)</span>, - maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, - legend <span class='op'>=</span> <span class='cn'>TRUE</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - col_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - pch_obs <span class='op'>=</span> <span class='st'>"auto"</span>, - frame <span class='op'>=</span> <span class='cn'>TRUE</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A fit represented in an <code><a href='mkinfit.html'>mkinfit</a></code> object.</p></td> - </tr> - <tr> - <th>obs_vars</th> - <td><p>A character vector of names of the observed variables for + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span> +<span> <span class="va">object</span>,</span> +<span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> +<span> xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1.1</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">data</span><span class="op">$</span><span class="va">time</span><span class="op">)</span><span class="op">)</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> xlab <span class="op">=</span> <span class="st">"Time"</span>,</span> +<span> ylab <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">standardized</span>, <span class="st">"Standardized residual"</span>, <span class="st">"Residual"</span><span class="op">)</span>,</span> +<span> maxabs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legend <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> lpos <span class="op">=</span> <span class="st">"topright"</span>,</span> +<span> col_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> pch_obs <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> frame <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> + + +<dt>obs_vars</dt> +<dd><p>A character vector of names of the observed variables for which residuals should be plotted. Defaults to all observed variables in -the model</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>plot range in x direction.</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized by dividing by the -standard deviation given by the error model of the fit?</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>Label for the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>maxabs</th> - <td><p>Maximum absolute value of the residuals. This is used for the -scaling of the y axis and defaults to "auto".</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be plotted?</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Where should the legend be placed? Default is "topright". Will -be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code>.</p></td> - </tr> - <tr> - <th>col_obs</th> - <td><p>Colors for the observed variables.</p></td> - </tr> - <tr> - <th>pch_obs</th> - <td><p>Symbols to be used for the observed variables.</p></td> - </tr> - <tr> - <th>frame</th> - <td><p>Should a frame be drawn around the plots?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>Nothing is returned by this function, as it is called for its side -effect, namely to produce a plot.</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +the model</p></dd> - <div class='dont-index'><p><code><a href='mkinplot.html'>mkinplot</a></code>, for a way to plot the data and the fitted -lines of the mkinfit object, and <code><a href='plot.mkinfit.html'>plot_res</a></code> for a function -combining the plot of the fit and the residual plot.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> +<dt>xlim</dt> +<dd><p>plot range in x direction.</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized by dividing by the +standard deviation given by the error model of the fit?</p></dd> + + +<dt>xlab</dt> +<dd><p>Label for the x axis.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>maxabs</dt> +<dd><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></dd> + + +<dt>legend</dt> +<dd><p>Should a legend be plotted?</p></dd> + + +<dt>lpos</dt> +<dd><p>Where should the legend be placed? Default is "topright". Will +be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="external-link">legend</a></code>.</p></dd> + + +<dt>col_obs</dt> +<dd><p>Colors for the observed variables.</p></dd> + + +<dt>pch_obs</dt> +<dd><p>Symbols to be used for the observed variables.</p></dd> + + +<dt>frame</dt> +<dd><p>Should a frame be drawn around the plots?</p></dd> + + +<dt>...</dt> +<dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>Nothing is returned by this function, as it is called for its side +effect, namely to produce a plot.</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted +lines of the mkinfit object, and <code><a href="plot.mkinfit.html">plot_res</a></code> for a function +combining the plot of the fit and the residual plot.</p></div> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke and Katrin Lindenberger</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"m1"</span><span class='op'>)</span>, m1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>FOCUS_2006_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'>mkinresplot</span><span class='op'>(</span><span class='va'>fit</span>, <span class='st'>"m1"</span><span class='op'>)</span> -</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span><span class="fu">mkinresplot</span><span class="op">(</span><span class="va">fit</span>, <span class="st">"m1"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mkinresplot-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/mmkin-1.png b/docs/dev/reference/mmkin-1.png Binary files differindex 701a6d6a..8ad9c11d 100644 --- a/docs/dev/reference/mmkin-1.png +++ b/docs/dev/reference/mmkin-1.png diff --git a/docs/dev/reference/mmkin-2.png b/docs/dev/reference/mmkin-2.png Binary files differindex 5277b389..da2a48a8 100644 --- a/docs/dev/reference/mmkin-2.png +++ b/docs/dev/reference/mmkin-2.png diff --git a/docs/dev/reference/mmkin-3.png b/docs/dev/reference/mmkin-3.png Binary files differindex 2659cd61..10d3f35b 100644 --- a/docs/dev/reference/mmkin-3.png +++ b/docs/dev/reference/mmkin-3.png diff --git a/docs/dev/reference/mmkin-4.png b/docs/dev/reference/mmkin-4.png Binary files differindex ae16ee79..132380a8 100644 --- a/docs/dev/reference/mmkin-4.png +++ b/docs/dev/reference/mmkin-4.png diff --git a/docs/dev/reference/mmkin-5.png b/docs/dev/reference/mmkin-5.png Binary files differindex 2b9dc831..4bfcc55e 100644 --- a/docs/dev/reference/mmkin-5.png +++ b/docs/dev/reference/mmkin-5.png diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index c385bbf6..5aa259f9 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ datasets specified in its first two arguments." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.5</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,213 +44,225 @@ datasets specified in its first two arguments." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>mmkin.Rd</code></div> </div> <div class="ref-description"> - <p>This function calls <code><a href='mkinfit.html'>mkinfit</a></code> on all combinations of models and + <p>This function calls <code><a href="mkinfit.html">mkinfit</a></code> on all combinations of models and datasets specified in its first two arguments.</p> </div> - <pre class="usage"><span class='fu'>mmkin</span><span class='op'>(</span> - models <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='va'>datasets</span>, - cores <span class='op'>=</span> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/Sys.info.html'>Sys.info</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>[</span><span class='st'>"sysname"</span><span class='op'>]</span> <span class='op'>==</span> <span class='st'>"Windows"</span><span class='op'>)</span> <span class='fl'>1</span> <span class='kw'>else</span> <span class='fu'>parallel</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/r/parallel/detectCores.html'>detectCores</a></span><span class='op'>(</span><span class='op'>)</span>, - cluster <span class='op'>=</span> <span class='cn'>NULL</span>, - <span class='va'>...</span> -<span class='op'>)</span> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mmkin</span><span class="op">(</span></span> +<span> models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> +<span> <span class="va">datasets</span>,</span> +<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span> +<span> cluster <span class="op">=</span> <span class="cn">NULL</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>models</dt> +<dd><p>Either a character vector of shorthand names like +<code>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</code>, or an optionally named +list of <code><a href="mkinmod.html">mkinmod</a></code> objects.</p></dd> + -<span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span></pre> +<dt>datasets</dt> +<dd><p>An optionally named list of datasets suitable as observed +data for <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>models</th> - <td><p>Either a character vector of shorthand names like -<code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named -list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td> - </tr> - <tr> - <th>datasets</th> - <td><p>An optionally named list of datasets suitable as observed -data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>cores</th> - <td><p>The number of cores to be used for multicore processing. This + +<dt>cores</dt> +<dd><p>The number of cores to be used for multicore processing. This is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows machines, cores > 1 is not supported, you need to use the <code>cluster</code> argument to use multiple logical processors. Per default, all cores -detected by <code><a href='https://rdrr.io/r/parallel/detectCores.html'>parallel::detectCores()</a></code> are used, except on Windows where -the default is 1.</p></td> - </tr> - <tr> - <th>cluster</th> - <td><p>A cluster as returned by <code>makeCluster</code> to be used -for parallel execution.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used.</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An mmkin object.</p></td> - </tr> - </table> +detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where +the default is 1.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A two-dimensional <code><a href='https://rdrr.io/r/base/array.html'>array</a></code> of <code><a href='mkinfit.html'>mkinfit</a></code> -objects and/or try-errors that can be indexed using the model names for the -first index (row index) and the dataset names for the second index (column -index).</p> - <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> +<dt>cluster</dt> +<dd><p>A cluster as returned by <code>makeCluster</code> to be used +for parallel execution.</p></dd> - <div class='dont-index'><p><code><a href='[.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for -plotting.</p></div> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - <p>Johannes Ranke</p> +<dt>...</dt> +<dd><p>Not used.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='co'># \dontrun{</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_FOMC_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>models</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>SFO_lin <span class='op'>=</span> <span class='va'>m_synth_SFO_lin</span>, FOMC_lin <span class='op'>=</span> <span class='va'>m_synth_FOMC_lin</span><span class='op'>)</span> -<span class='va'>datasets</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>datasets</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='st'>"Dataset"</span>, <span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>)</span> -<span class='va'>time_default</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.0</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> -<span class='va'>time_1</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span><span class='op'>(</span><span class='va'>fits.4</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='va'>models</span>, <span class='va'>datasets</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span><span class='op'>)</span> +<dt>x</dt> +<dd><p>An mmkin object.</p></dd> -<span class='va'>time_default</span> -</div><div class='output co'>#> user system elapsed -#> 4.771 0.576 1.803 </div><div class='input'><span class='va'>time_1</span> -</div><div class='output co'>#> user system elapsed -#> 5.779 0.000 5.781 </div><div class='input'> -<span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340481 0.2659519 0.7505683 0.2494317 -#> -#> $distimes -#> DT50 DT90 -#> parent 0.877769 2.915885 -#> M1 2.325744 7.725956 -#> M2 33.720100 112.015749 -#> </div><div class='input'> -<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='op'>]</span>, obs_var <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> -<span class='co'># by plot.mkinfit and can be plotted using plot_sep</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span>, sep_obs <span class='op'>=</span> <span class='cn'>TRUE</span>, show_residuals <span class='op'>=</span> <span class='cn'>TRUE</span>, show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>)</span> -<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> -<span class='co'># allow to plot the observed variables separately</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits.0</span><span class='op'>[</span><span class='fl'>1</span>, <span class='fl'>1</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> -<span class='co'># On Windows, we can use multiple cores by making a cluster using the parallel</span> -<span class='co'># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span> -<span class='va'>cl</span> <span class='op'><-</span> <span class='fu'>makePSOCKcluster</span><span class='op'>(</span><span class='fl'>12</span><span class='op'>)</span> -<span class='va'>f</span> <span class='op'><-</span> <span class='fu'>mmkin</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>A <span class='op'>=</span> <span class='va'>FOCUS_2006_A</span>, B <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, C <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span>, D <span class='op'>=</span> <span class='va'>FOCUS_2006_D</span><span class='op'>)</span>, - cluster <span class='op'>=</span> <span class='va'>cl</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> <mmkin> object -#> Status of individual fits: -#> -#> dataset -#> model A B C D -#> SFO OK OK OK OK -#> FOMC OK OK OK OK -#> DFOP OK OK OK OK -#> -#> OK: No warnings</div><div class='input'><span class='co'># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span> -<span class='co'># dataset is really SFO, and the FOMC fit is overparameterised</span> -<span class='fu'>stopCluster</span><span class='op'>(</span><span class='va'>cl</span><span class='op'>)</span> -<span class='co'># }</span> +</dl></div> + <div id="value"> + <h2>Value</h2> + -</div></pre> +<p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code></p> + + +<p>objects and/or try-errors that can be indexed using the model names for the +first index (row index) and the dataset names for the second index (column +index).</p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><p><code><a href="Extract.mmkin.html">[.mmkin</a></code> for subsetting, <code><a href="plot.mmkin.html">plot.mmkin</a></code> for +plotting.</p></div> + </div> + <div id="author"> + <h2>Author</h2> + <p>Johannes Ranke</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_FOMC_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">models</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">datasets</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">datasets</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.0</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">time_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">fits.4</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">time_default</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 7.113 0.837 2.580 </span> +<span class="r-in"><span><span class="va">time_1</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> +<span class="r-out co"><span class="r-pr">#></span> 5.617 0.008 5.626 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_M1 parent_sink M1_M2 M1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505683 0.2494317 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.877769 2.915885</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.325744 7.725956</span> +<span class="r-out co"><span class="r-pr">#></span> M2 33.720100 112.015749</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span></span> +<span class="r-in"><span><span class="co"># by plot.mkinfit and can be plotted using plot_sep</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span></span> +<span class="r-in"><span><span class="co"># allow to plot the observed variables separately</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span></span> +<span class="r-in"><span><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span></span> +<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">makePSOCKcluster</span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in makePSOCKcluster(12):</span> could not find function "makePSOCKcluster"</span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</span>, B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> cluster <span class="op">=</span> <span class="va">cl</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in system.time({ if (is.null(cluster)) { results <- parallel::mclapply(as.list(1:n.fits), fit_function, mc.cores = cores, mc.preschedule = FALSE) } else { results <- parallel::parLapply(cluster, as.list(1:n.fits), fit_function) }}):</span> object 'cl' not found</span> +<span class="r-msg co"><span class="r-pr">#></span> Timing stopped at: 0 0 0.001</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in print(f):</span> object 'f' not found</span> +<span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span> +<span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span> +<span class="r-in"><span><span class="fu">stopCluster</span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in stopCluster(cl):</span> could not find function "stopCluster"</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/multistart-1.png b/docs/dev/reference/multistart-1.png Binary files differindex 7fc24a04..dcd493c9 100644 --- a/docs/dev/reference/multistart-1.png +++ b/docs/dev/reference/multistart-1.png diff --git a/docs/dev/reference/multistart-2.png b/docs/dev/reference/multistart-2.png Binary files differindex 7553a51a..e1983f12 100644 --- a/docs/dev/reference/multistart-2.png +++ b/docs/dev/reference/multistart-2.png diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 3f5c4b35..0f2988bd 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -64,7 +64,10 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/nafta-1.png b/docs/dev/reference/nafta-1.png Binary files differindex 4f0d7833..5d2d434b 100644 --- a/docs/dev/reference/nafta-1.png +++ b/docs/dev/reference/nafta-1.png diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html index 6fb797a5..eafbca7f 100644 --- a/docs/dev/reference/nafta.html +++ b/docs/dev/reference/nafta.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Evaluate parent kinetics using the NAFTA guidance — nafta • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script 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src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Evaluate parent kinetics using the NAFTA guidance — nafta"><meta property="og:description" content="The function fits the SFO, IORE and DFOP models using mmkin and returns an object of class nafta that has methods for printing and plotting. Print nafta objects. The results for the three models are printed in the -order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,188 +45,198 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Evaluate parent kinetics using the NAFTA guidance</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> <div class="hidden name"><code>nafta.Rd</code></div> </div> <div class="ref-description"> - <p>The function fits the SFO, IORE and DFOP models using <code><a href='mmkin.html'>mmkin</a></code> + <p>The function fits the SFO, IORE and DFOP models using <code><a href="mmkin.html">mmkin</a></code> and returns an object of class <code>nafta</code> that has methods for printing and plotting.</p> <p>Print nafta objects. The results for the three models are printed in the order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p> </div> - <pre class="usage"><span class='fu'>nafta</span><span class='op'>(</span><span class='va'>ds</span>, title <span class='op'>=</span> <span class='cn'>NA</span>, quiet <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span> - -<span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>x</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, digits <span class='op'>=</span> <span class='fl'>3</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>ds</th> - <td><p>A dataframe that must contain one variable called "time" with the -time values specified by the <code>time</code> argument, one column called -"name" with the grouping of the observed values, and finally one column of -observed values called "value".</p></td> - </tr> - <tr> - <th>title</th> - <td><p>Optional title of the dataset</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should the evaluation text be shown?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='mmkin.html'>mmkin</a></code> (not for the -printing method).</p></td> - </tr> - <tr> - <th>x</th> - <td><p>An <code>nafta</code> object.</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to be used for printing parameters and -dissipation times.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> +<span></span> +<span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="source"> + <h2>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides -<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> +<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> accessed 2019-02-22</p> <p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-life Values and Characterizing Pesticide Degradation -<a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>ds</dt> +<dd><p>A dataframe that must contain one variable called "time" with the +time values specified by the <code>time</code> argument, one column called +"name" with the grouping of the observed values, and finally one column of +observed values called "value".</p></dd> + + +<dt>title</dt> +<dd><p>Optional title of the dataset</p></dd> + - <p>An list of class <code>nafta</code>. The list element named "mmkin" is the -<code><a href='mmkin.html'>mmkin</a></code> object containing the fits of the three models. The +<dt>quiet</dt> +<dd><p>Should the evaluation text be shown?</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="mmkin.html">mmkin</a></code> (not for the +printing method).</p></dd> + + +<dt>x</dt> +<dd><p>An <code>nafta</code> object.</p></dd> + + +<dt>digits</dt> +<dd><p>Number of digits to be used for printing parameters and +dissipation times.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>An list of class <code>nafta</code>. The list element named "mmkin" is the +<code><a href="mmkin.html">mmkin</a></code> object containing the fits of the three models. The list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='va'>nafta_evaluation</span> <span class='op'><-</span> <span class='fu'>nafta</span><span class='op'>(</span><span class='va'>NAFTA_SOP_Appendix_D</span>, cores <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> -#> Critical sum of squares for checking the SFO model: -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.7558 1.80e-14 77.18268 90.3288 -#> k_parent 0.0017 7.43e-05 0.00112 0.0026 -#> sigma 8.7518 1.22e-05 5.64278 11.8608 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 -#> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 -#> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 -#> sigma 5.85e+00 NA 3.76e+00 7.94e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 -#> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 -#> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 -#> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 -#> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 -#> -#> Representative half-life: -#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>nafta_evaluation</span><span class='op'>)</span> -</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> +<span class="r-msg co"><span class="r-pr">#></span> to the terminal degradation rate found with the DFOP model.</span> +<span class="r-msg co"><span class="r-pr">#></span> The representative half-life obtained from the DFOP model may be used</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Sums of squares:</span> +<span class="r-out co"><span class="r-pr">#></span> SFO IORE DFOP </span> +<span class="r-out co"><span class="r-pr">#></span> 1378.6832 615.7730 517.8836 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Critical sum of squares for checking the SFO model:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 717.4598</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> $SFO</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 83.7558 1.80e-14 77.18268 90.3288</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0017 7.43e-05 0.00112 0.0026</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.7518 1.22e-05 5.64278 11.8608</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $IORE</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.69e+01 NA 8.88e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09</span> +<span class="r-out co"><span class="r-pr">#></span> N_parent 6.68e+00 NA 4.19e+00 9.17e+00</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.85e+00 NA 3.76e+00 7.94e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $DFOP</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03</span> +<span class="r-out co"><span class="r-pr">#></span> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> DTx values:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50_rep</span> +<span class="r-out co"><span class="r-pr">#></span> SFO 407 1350 407</span> +<span class="r-out co"><span class="r-pr">#></span> IORE 541 5190000 1560000</span> +<span class="r-out co"><span class="r-pr">#></span> DFOP 429 2380 841</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Representative half-life:</span> +<span class="r-out co"><span class="r-pr">#></span> [1] 841.41</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">nafta_evaluation</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="nafta-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png Binary files differindex 67cc7f3c..c4fc9d31 100644 --- a/docs/dev/reference/nlme-1.png +++ b/docs/dev/reference/nlme-1.png diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png Binary files differindex bb1e6f81..d9512f41 100644 --- a/docs/dev/reference/nlme-2.png +++ b/docs/dev/reference/nlme-2.png diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index e7844299..b8b36d56 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -29,7 +29,7 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> @@ -44,19 +44,28 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -90,20 +99,25 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span> - -<span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span> +<span></span> +<span><span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> <h2>Arguments</h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>A function that can be used with nlme -A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> + + +<p>A function that can be used with nlme</p> + + +<p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> </div> <div id="see-also"> <h2>See also</h2> @@ -112,78 +126,78 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span> -<span class="r-in"><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> -<span class="r-in"><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="co"># These assignments are necessary for these objects to be</span></span> -<span class="r-in"><span class="co"># visible to nlme and augPred when evaluation is done by</span></span> -<span class="r-in"><span class="co"># pkgdown to generate the html docs.</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span> -<span class="r-in"></span> -<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span> -<span class="r-in"><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span> -<span class="r-in"> data <span class="op">=</span> <span class="va">grouped_data</span>,</span> -<span class="r-in"> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span> -<span class="r-in"> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span> -<span class="r-in"> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">98</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_1_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">102</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_2_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">103</span><span class="op">)</span>, <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_SFO_3_long</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d1</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_1</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d2</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_2</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d3</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_SFO_3</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">4</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>d1 <span class="op">=</span> <span class="va">d1</span>, d2 <span class="op">=</span> <span class="va">d2</span>, d3 <span class="op">=</span> <span class="va">d3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">mean_dp</span> <span class="op"><-</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">grouped_data</span> <span class="op"><-</span> <span class="fu">nlme_data</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">nlme_f</span> <span class="op"><-</span> <span class="fu">nlme_function</span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># These assignments are necessary for these objects to be</span></span></span> +<span class="r-in"><span><span class="co"># visible to nlme and augPred when evaluation is done by</span></span></span> +<span class="r-in"><span><span class="co"># pkgdown to generate the html docs.</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"nlme_f"</span>, <span class="va">nlme_f</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="st">"grouped_data"</span>, <span class="va">grouped_data</span>, <span class="fu"><a href="https://rdrr.io/r/base/environment.html" class="external-link">globalenv</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">m_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu">nlme_f</span><span class="op">(</span><span class="va">name</span>, <span class="va">time</span>, <span class="va">parent_0</span>, <span class="va">log_k_parent_sink</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">grouped_data</span>,</span></span> +<span class="r-in"><span> fixed <span class="op">=</span> <span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span>,</span></span> +<span class="r-in"><span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">parent_0</span> <span class="op">+</span> <span class="va">log_k_parent_sink</span> <span class="op">~</span> <span class="fl">1</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="va">mean_dp</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m_nlme</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Nonlinear mixed-effects model fit by maximum likelihood</span> <span class="r-out co"><span class="r-pr">#></span> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) </span> <span class="r-out co"><span class="r-pr">#></span> Data: grouped_data </span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 300.6824 310.2426 -145.3412</span> +<span class="r-out co"><span class="r-pr">#></span> 266.6428 275.8935 -128.3214</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)</span> <span class="r-out co"><span class="r-pr">#></span> Level: ds</span> <span class="r-out co"><span class="r-pr">#></span> Structure: Diagonal</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> -<span class="r-out co"><span class="r-pr">#></span> StdDev: 1.697361 0.6801209 3.666073</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink Residual</span> +<span class="r-out co"><span class="r-pr">#></span> StdDev: 0.000368491 0.7058039 3.065183</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects: parent_0 + log_k_parent_sink ~ 1 </span> -<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.99378 1.3890416 46 72.70753 0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0</span> +<span class="r-out co"><span class="r-pr">#></span> Value Std.Error DF t-value p-value</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.18323 0.7900461 43 128.07257 0</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0</span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> prnt_0</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.027 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink 0.031 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Standardized Within-Group Residuals:</span> -<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> -<span class="r-out co"><span class="r-pr">#></span> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 </span> +<span class="r-out co"><span class="r-pr">#></span> Min Q1 Med Q3 Max </span> +<span class="r-out co"><span class="r-pr">#></span> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 50</span> +<span class="r-out co"><span class="r-pr">#></span> Number of Observations: 47</span> <span class="r-out co"><span class="r-pr">#></span> Number of Groups: 3 </span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/augPred.html" class="external-link">augPred</a></span><span class="op">(</span><span class="va">m_nlme</span>, level <span class="op">=</span> <span class="fl">0</span><span class="op">:</span><span class="fl">1</span><span class="op">)</span>, layout <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-1.png" alt="" width="700" height="433"></span> -<span class="r-in"><span class="co"># augPred does not work on fits with more than one state</span></span> -<span class="r-in"><span class="co"># variable</span></span> -<span class="r-in"><span class="co">#</span></span> -<span class="r-in"><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span> -<span class="r-in"><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span> -<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span> +<span class="r-in"><span><span class="co"># augPred does not work on fits with more than one state</span></span></span> +<span class="r-in"><span><span class="co"># variable</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># The procedure is greatly simplified by the nlme.mmkin function</span></span></span> +<span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlme</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> </code></pre></div> </div> @@ -199,7 +213,7 @@ A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external- </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> </footer></div> diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index 2bbadb88..8c069470 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -46,19 +46,25 @@ have been obtained by fitting the same model to a list of datasets."><meta name= <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -97,7 +103,7 @@ have been obtained by fitting the same model to a list of datasets.</p> <span> data <span class="op">=</span> <span class="st">"auto"</span>,</span> <span> fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span></span> <span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,</span> -<span> random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> +<span> random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,</span> <span> <span class="va">groups</span>,</span> <span> start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span> <span> correlation <span class="op">=</span> <span class="cn">NULL</span>,</span> diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html index 0b6c963c..8c2d04f0 100644 --- a/docs/dev/reference/nobs.mkinfit.html +++ b/docs/dev/reference/nobs.mkinfit.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" 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data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Number of observations on which an mkinfit object was fitted</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nobs.mkinfit.R'><code>R/nobs.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nobs.mkinfit.R" class="external-link"><code>R/nobs.mkinfit.R</code></a></small> <div class="hidden name"><code>nobs.mkinfit.Rd</code></div> </div> @@ -147,51 +92,49 @@ <p>Number of observations on which an mkinfit object was fitted</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/nobs.html" class="external-link">nobs</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An mkinfit object</p></dd> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An mkinfit object</p></td> - </tr> - <tr> - <th>...</th> - <td><p>For compatibility with the generic method</p></td> - </tr> - </table> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>...</dt> +<dd><p>For compatibility with the generic method</p></dd> - <p>The number of rows in the data included in the mkinfit object</p> +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The number of rows in the data included in the mkinfit object</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 95db0593..b0385c8a 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><meta nam </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ without considering the error structure that was assumed for the fit."><meta nam <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index ffe93e6c..9852b694 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -61,7 +61,10 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -134,6 +137,12 @@ If 'median', parameters are scaled using the median parameters from all fits.</p <dd><p>Title of the plot</p></dd> </dl></div> + <div id="details"> + <h2>Details</h2> + <p>Starting values of degradation model parameters and error model parameters +are shown as green circles. The results obtained in the original run +are shown as red circles.</p> + </div> <div id="references"> <h2>References</h2> <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index b1c62721..4bd170a1 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index 764f0699..d125a606 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -46,19 +46,25 @@ observed data together with the solution of the fitted model."><meta name="robot <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/plot.mmkin-1.png b/docs/dev/reference/plot.mmkin-1.png Binary files differindex 647dfb8a..235e33a7 100644 --- a/docs/dev/reference/plot.mmkin-1.png +++ b/docs/dev/reference/plot.mmkin-1.png diff --git a/docs/dev/reference/plot.mmkin-2.png b/docs/dev/reference/plot.mmkin-2.png Binary files differindex 1bc1c9db..7af84edf 100644 --- a/docs/dev/reference/plot.mmkin-2.png +++ b/docs/dev/reference/plot.mmkin-2.png diff --git a/docs/dev/reference/plot.mmkin-3.png b/docs/dev/reference/plot.mmkin-3.png Binary files differindex 50d6ffac..56bfac50 100644 --- a/docs/dev/reference/plot.mmkin-3.png +++ b/docs/dev/reference/plot.mmkin-3.png diff --git a/docs/dev/reference/plot.mmkin-4.png b/docs/dev/reference/plot.mmkin-4.png Binary files differindex e049fa16..5da05f40 100644 --- a/docs/dev/reference/plot.mmkin-4.png +++ b/docs/dev/reference/plot.mmkin-4.png diff --git a/docs/dev/reference/plot.mmkin-5.png b/docs/dev/reference/plot.mmkin-5.png Binary files differindex 2421995b..3ec224f4 100644 --- a/docs/dev/reference/plot.mmkin-5.png +++ b/docs/dev/reference/plot.mmkin-5.png diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html index 9ca0df94..09f311c5 100644 --- a/docs/dev/reference/plot.mmkin.html +++ b/docs/dev/reference/plot.mmkin.html @@ -1,71 +1,16 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -76,23 +21,21 @@ the fit of at least one model to the same dataset is shown." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -102,200 +45,210 @@ the fit of at least one model to the same dataset is shown." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mmkin.R" class="external-link"><code>R/plot.mmkin.R</code></a></small> <div class="hidden name"><code>plot.mmkin.Rd</code></div> </div> <div class="ref-description"> - <p>When x is a row selected from an mmkin object (<code><a href='[.mmkin.html'>[.mmkin</a></code>), the + <p>When x is a row selected from an mmkin object (<code><a href="Extract.mmkin.html">[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> </div> - <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> - <span class='va'>x</span>, - main <span class='op'>=</span> <span class='st'>"auto"</span>, - legends <span class='op'>=</span> <span class='fl'>1</span>, - resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"time"</span>, <span class='st'>"errmod"</span><span class='op'>)</span>, - ylab <span class='op'>=</span> <span class='st'>"Residue"</span>, - standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, - show_errmin <span class='op'>=</span> <span class='cn'>TRUE</span>, - errmin_var <span class='op'>=</span> <span class='st'>"All data"</span>, - errmin_digits <span class='op'>=</span> <span class='fl'>3</span>, - cex <span class='op'>=</span> <span class='fl'>0.7</span>, - rel.height.middle <span class='op'>=</span> <span class='fl'>0.9</span>, - ymax <span class='op'>=</span> <span class='st'>"auto"</span>, - <span class='va'>...</span> -<span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of class <code><a href='mmkin.html'>mmkin</a></code>, with either one row or one -column.</p></td> - </tr> - <tr> - <th>main</th> - <td><p>The main title placed on the outer margin of the plot.</p></td> - </tr> - <tr> - <th>legends</th> - <td><p>An index for the fits for which legends should be shown.</p></td> - </tr> - <tr> - <th>resplot</th> - <td><p>Should the residuals plotted against time, using -<code><a href='mkinresplot.html'>mkinresplot</a></code>, or as squared residuals against predicted -values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot</a></code>.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>Label for the y axis.</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized? This option -is passed to <code><a href='mkinresplot.html'>mkinresplot</a></code>, it only takes effect if -<code>resplot = "time"</code>.</p></td> - </tr> - <tr> - <th>show_errmin</th> - <td><p>Should the chi2 error level be shown on top of the plots -to the left?</p></td> - </tr> - <tr> - <th>errmin_var</th> - <td><p>The variable for which the FOCUS chi2 error value should -be shown.</p></td> - </tr> - <tr> - <th>errmin_digits</th> - <td><p>The number of significant digits for rounding the FOCUS -chi2 error percentage.</p></td> - </tr> - <tr> - <th>cex</th> - <td><p>Passed to the plot functions and <code><a href='https://rdrr.io/r/graphics/mtext.html'>mtext</a></code>.</p></td> - </tr> - <tr> - <th>rel.height.middle</th> - <td><p>The relative height of the middle plot, if more -than two rows of plots are shown.</p></td> - </tr> - <tr> - <th>ymax</th> - <td><p>Maximum y axis value for <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code>.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and -<code><a href='mkinresplot.html'>mkinresplot</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>If the current plot device is a <code><a href='https://rdrr.io/pkg/tikzDevice/man/tikz.html'>tikz</a></code> device, then -latex is being used for the formatting of the chi2 error level.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legends <span class="op">=</span> <span class="fl">1</span>,</span> +<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span> +<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span> +<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span> +<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one +column.</p></dd> + + +<dt>main</dt> +<dd><p>The main title placed on the outer margin of the plot.</p></dd> + + +<dt>legends</dt> +<dd><p>An index for the fits for which legends should be shown.</p></dd> + + +<dt>resplot</dt> +<dd><p>Should the residuals plotted against time, using +<code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted +values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd> + + +<dt>ylab</dt> +<dd><p>Label for the y axis.</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized? This option +is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if +<code>resplot = "time"</code>.</p></dd> + + +<dt>show_errmin</dt> +<dd><p>Should the chi2 error level be shown on top of the plots +to the left?</p></dd> + + +<dt>errmin_var</dt> +<dd><p>The variable for which the FOCUS chi2 error value should +be shown.</p></dd> + +<dt>errmin_digits</dt> +<dd><p>The number of significant digits for rounding the FOCUS +chi2 error percentage.</p></dd> + + +<dt>cex</dt> +<dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd> + + +<dt>rel.height.middle</dt> +<dd><p>The relative height of the middle plot, if more +than two rows of plots are shown.</p></dd> + + +<dt>ymax</dt> +<dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and +<code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function is called for its side effect.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then +latex is being used for the formatting of the chi2 error level.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> - <span class='co'># \dontrun{</span> - <span class='co'># Only use one core not to offend CRAN checks</span> - <span class='va'>fits</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"HS"</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"FOCUS B"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='op'>=</span> <span class='va'>FOCUS_2006_C</span><span class='op'>)</span>, <span class='co'># named list for titles</span> - cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Optimisation did not converge:</span> -#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, show_errmin <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span> - <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> - <span class='co'># generated by pkgdown, as far as I know).</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># same as plot(fits[1, 2])</span> -</div><div class='img'><img src='plot.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='co'># Show the error models</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>fits</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span>, resplot <span class='op'>=</span> <span class='st'>"errmod"</span><span class='op'>)</span> -</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> +<span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span> +<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span> +<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Show the error models</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html index c24fba99..82b46336 100644 --- a/docs/dev/reference/plot.nafta.html +++ b/docs/dev/reference/plot.nafta.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - 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- - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ function (SFO, then IORE, then DFOP)." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ function (SFO, then IORE, then DFOP)." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot the results of the three models used in the NAFTA scheme.</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> <div class="hidden name"><code>plot.nafta.Rd</code></div> </div> @@ -149,65 +94,65 @@ function (SFO, then IORE, then DFOP)." /> function (SFO, then IORE, then DFOP).</p> </div> - <pre class="usage"><span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>x</span>, legend <span class='op'>=</span> <span class='cn'>FALSE</span>, main <span class='op'>=</span> <span class='st'>"auto"</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>x</th> - <td><p>An object of class <code><a href='nafta.html'>nafta</a></code>.</p></td> - </tr> - <tr> - <th>legend</th> - <td><p>Should a legend be added?</p></td> - </tr> - <tr> - <th>main</th> - <td><p>Possibility to override the main title of the plot.</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Further arguments passed to <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function is called for its side effect.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - - <p>Calls <code><a href='plot.mmkin.html'>plot.mmkin</a></code>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nafta</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, legend <span class="op">=</span> <span class="cn">FALSE</span>, main <span class="op">=</span> <span class="st">"auto"</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>An object of class <code><a href="nafta.html">nafta</a></code>.</p></dd> + +<dt>legend</dt> +<dd><p>Should a legend be added?</p></dd> + + +<dt>main</dt> +<dd><p>Possibility to override the main title of the plot.</p></dd> + + +<dt>...</dt> +<dd><p>Further arguments passed to <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function is called for its side effect.</p> + </div> + <div id="details"> + <h2>Details</h2> + <p>Calls <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html index efba012b..d0ac47d4 100644 --- a/docs/dev/reference/read_spreadsheet.html +++ b/docs/dev/reference/read_spreadsheet.html @@ -22,7 +22,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html index 0999e346..ad825391 100644 --- a/docs/dev/reference/reexports.html +++ b/docs/dev/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -55,19 +55,25 @@ intervals, nlme <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html index 3f518ab7..009f790f 100644 --- a/docs/dev/reference/residuals.mkinfit.html +++ b/docs/dev/reference/residuals.mkinfit.html @@ -1,67 +1,12 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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- +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -72,23 +17,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -98,48 +41,50 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Extract residuals from an mkinfit model</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/residuals.mkinfit.R'><code>R/residuals.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/residuals.mkinfit.R" class="external-link"><code>R/residuals.mkinfit.R</code></a></small> <div class="hidden name"><code>residuals.mkinfit.Rd</code></div> </div> @@ -147,60 +92,59 @@ <p>Extract residuals from an mkinfit model</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>object</span>, standardized <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>A <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td> - </tr> - <tr> - <th>standardized</th> - <td><p>Should the residuals be standardized by dividing by the -standard deviation obtained from the fitted error model?</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Not used</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 -#> [7] -0.03269080 1.45347823 -0.88423697</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/residuals.html'>residuals</a></span><span class='op'>(</span><span class='va'>f</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 -#> [7] -0.04695355 2.08761977 -1.27002287</div></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">object</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> + + +<dt>standardized</dt> +<dd><p>Should the residuals be standardized by dividing by the +standard deviation obtained from the fitted error model?</p></dd> + + +<dt>...</dt> +<dd><p>Not used</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702</span> +<span class="r-out co"><span class="r-pr">#></span> [7] -0.03269080 1.45347823 -0.88423697</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208</span> +<span class="r-out co"><span class="r-pr">#></span> [7] -0.04695355 2.08761977 -1.27002287</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index d2e930e1..d18cb848 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -113,7 +113,7 @@ Expectation Maximisation algorithm (SAEM).</p> <span> covariates <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> covariate_models <span class="op">=</span> <span class="cn">NULL</span>,</span> <span> no_random_effect <span class="op">=</span> <span class="cn">NULL</span>,</span> -<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fl">0.1</span><span class="op">)</span>,</span> +<span> error.init <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">)</span>,</span> <span> nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">300</span>, <span class="fl">100</span><span class="op">)</span>,</span> <span> control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>displayProgress <span class="op">=</span> <span class="cn">FALSE</span>, print <span class="op">=</span> <span class="cn">FALSE</span>, nbiter.saemix <span class="op">=</span> <span class="va">nbiter.saemix</span>,</span> <span> save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span> @@ -430,10 +430,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Nov 16 10:49:43 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Nov 16 10:49:43 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:00 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:01 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -448,7 +448,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.935 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.778 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> diff --git a/docs/dev/reference/schaefer07_complex_case-1.png b/docs/dev/reference/schaefer07_complex_case-1.png Binary files differindex 96aab2dc..eee9e0cc 100644 --- a/docs/dev/reference/schaefer07_complex_case-1.png +++ b/docs/dev/reference/schaefer07_complex_case-1.png diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html index 4ccad5c4..5ff62d34 100644 --- a/docs/dev/reference/schaefer07_complex_case.html +++ b/docs/dev/reference/schaefer07_complex_case.html @@ -1,69 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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The results from the fitting are also included." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> + The results from the fitting are also included."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -74,23 +19,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -100,44 +43,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Metabolism data set used for checking the software quality of KinGUI</h1> @@ -151,93 +96,109 @@ The results from the fitting are also included.</p> </div> - <pre class="usage"><span class='va'>schaefer07_complex_case</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div> + </div> + + <div id="format"> + <h2>Format</h2> + <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl><dt><code>time</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>parent</code></dt> +<dd><p>a numeric vector</p></dd> + <dt><code>A1</code></dt> +<dd><p>a numeric vector</p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>B1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>C1</code></dt> +<dd><p>a numeric vector</p></dd> + + <dt><code>A2</code></dt> +<dd><p>a numeric vector</p></dd> - <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl> - <dt><code>time</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>parent</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>A1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>B1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>C1</code></dt><dd><p>a numeric vector</p></dd> - <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd> </dl><p>The results are a data frame with 14 results for different parameter values</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>data</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_case</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> -<span class='va'>model</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span><span class='op'>)</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - A1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"A2"</span><span class='op'>)</span>, - B1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - C1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - A2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='co'># \dontrun{</span> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>model</span>, <span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> $ff -#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink -#> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 -#> -#> $distimes -#> DT50 DT90 -#> parent 13.95078 46.34350 -#> A1 49.75342 165.27728 -#> B1 37.26908 123.80520 -#> C1 11.23131 37.30961 -#> A2 28.50624 94.69567 -#> </div><div class='input'> <span class='co'># }</span> - <span class='co'># Compare with the results obtained in the original publication</span> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>schaefer07_complex_results</span><span class='op'>)</span> -</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation -#> 1 parent degradation rate 0.0496 0.0506 2.0 -#> 2 parent DT50 13.9900 13.6900 2.2 -#> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9 -#> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2 -#> 5 metabolite A1 DT50 49.9600 50.8900 1.8 -#> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6 -#> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7 -#> 8 metabolite B1 DT50 39.6100 40.2400 1.6 -#> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5 -#> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9 -#> 11 metabolite C1 DT50 10.8700 9.9000 9.8 -#> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7 -#> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 -#> 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"A2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> B1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> C1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> A2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">model</span>, <span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="schaefer07_complex_case-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> $ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 0.3809620 0.1954667 0.4235713 0.0000000 0.4479619 0.5520381 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> $distimes</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 13.95078 46.34350</span> +<span class="r-out co"><span class="r-pr">#></span> A1 49.75342 165.27728</span> +<span class="r-out co"><span class="r-pr">#></span> B1 37.26908 123.80520</span> +<span class="r-out co"><span class="r-pr">#></span> C1 11.23131 37.30961</span> +<span class="r-out co"><span class="r-pr">#></span> A2 28.50624 94.69567</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span> <span class="co"># Compare with the results obtained in the original publication</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">schaefer07_complex_results</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> compound parameter KinGUI ModelMaker deviation</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent degradation rate 0.0496 0.0506 2.0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 parent DT50 13.9900 13.6900 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9</span> +<span class="r-out co"><span class="r-pr">#></span> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2</span> +<span class="r-out co"><span class="r-pr">#></span> 5 metabolite A1 DT50 49.9600 50.8900 1.8</span> +<span class="r-out co"><span class="r-pr">#></span> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6</span> +<span class="r-out co"><span class="r-pr">#></span> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7</span> +<span class="r-out co"><span class="r-pr">#></span> 8 metabolite B1 DT50 39.6100 40.2400 1.6</span> +<span class="r-out co"><span class="r-pr">#></span> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5</span> +<span class="r-out co"><span class="r-pr">#></span> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9</span> +<span class="r-out co"><span class="r-pr">#></span> 11 metabolite C1 DT50 10.8700 9.9000 9.8</span> +<span class="r-out co"><span class="r-pr">#></span> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7</span> +<span class="r-out co"><span class="r-pr">#></span> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4</span> +<span class="r-out co"><span class="r-pr">#></span> 14 metabolite A2 DT50 28.2400 28.4500 0.7</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 6c6a5d46..fab0a72d 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/sigma_twocomp-1.png b/docs/dev/reference/sigma_twocomp-1.png Binary files differindex 6e61684e..0353b72c 100644 --- a/docs/dev/reference/sigma_twocomp-1.png +++ b/docs/dev/reference/sigma_twocomp-1.png diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html index b7d295b2..292bf8e8 100644 --- a/docs/dev/reference/sigma_twocomp.html +++ b/docs/dev/reference/sigma_twocomp.html @@ -1,68 +1,13 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Two-component error model — sigma_twocomp • mkin</title> - - -<!-- jquery --> 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describing the standard deviation of the measurement error in +dependence of the measured value \(y\):"><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -73,23 +18,21 @@ dependence of the measured value \(y\):" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,48 +42,50 @@ dependence of the measured value \(y\):" /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Two-component error model</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/sigma_twocomp.R'><code>R/sigma_twocomp.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/sigma_twocomp.R" class="external-link"><code>R/sigma_twocomp.R</code></a></small> <div class="hidden name"><code>sigma_twocomp.Rd</code></div> </div> @@ -149,40 +94,43 @@ dependence of the measured value \(y\):" /> dependence of the measured value \(y\):</p> </div> - <pre class="usage"><span class='fu'>sigma_twocomp</span><span class='op'>(</span><span class='va'>y</span>, <span class='va'>sigma_low</span>, <span class='va'>rsd_high</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>y</th> - <td><p>The magnitude of the observed value</p></td> - </tr> - <tr> - <th>sigma_low</th> - <td><p>The asymptotic minimum of the standard deviation for low -observed values</p></td> - </tr> - <tr> - <th>rsd_high</th> - <td><p>The coefficient describing the increase of the standard -deviation with the magnitude of the observed value</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The standard deviation of the response variable.</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>y</dt> +<dd><p>The magnitude of the observed value</p></dd> + +<dt>sigma_low</dt> +<dd><p>The asymptotic minimum of the standard deviation for low +observed values</p></dd> + + +<dt>rsd_high</dt> +<dd><p>The coefficient describing the increase of the standard +deviation with the magnitude of the observed value</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The standard deviation of the response variable.</p> + </div> + <div id="details"> + <h2>Details</h2> <p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)</p> <p>This is the error model used for example by Werner et al. (1978). The model proposed by Rocke and Lorenzato (1995) can be written in this form as well, but assumes approximate lognormal distribution of errors for high values of y.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - + </div> + <div id="references"> + <h2>References</h2> <p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.</p> @@ -190,61 +138,62 @@ Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical Degradation Data. <em>Environments</em> 6(12) 124 -doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6120124</a> +<a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='va'>times</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> -<span class='va'>d_pred</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>time <span class='op'>=</span> <span class='va'>times</span>, parent <span class='op'>=</span> <span class='fl'>100</span> <span class='op'>*</span> <span class='fu'><a href='https://rdrr.io/r/base/Log.html'>exp</a></span><span class='op'>(</span><span class='op'>-</span> <span class='fl'>0.03</span> <span class='op'>*</span> <span class='va'>times</span><span class='op'>)</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/Random.html'>set.seed</a></span><span class='op'>(</span><span class='fl'>123456</span><span class='op'>)</span> -<span class='va'>d_syn</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_pred</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>y</span><span class='op'>)</span> <span class='fu'>sigma_twocomp</span><span class='op'>(</span><span class='va'>y</span>, <span class='fl'>1</span>, <span class='fl'>0.07</span><span class='op'>)</span>, - reps <span class='op'>=</span> <span class='fl'>2</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> -<span class='va'>f_nls</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/nls.html'>nls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, data <span class='op'>=</span> <span class='va'>d_syn</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> -<span class='va'>f_gnls</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/gnls.html'>gnls</a></span><span class='op'>(</span><span class='va'>value</span> <span class='op'>~</span> <span class='fu'><a href='https://rdrr.io/r/stats/SSasymp.html'>SSasymp</a></span><span class='op'>(</span><span class='va'>time</span>, <span class='fl'>0</span>, <span class='va'>parent_0</span>, <span class='va'>lrc</span><span class='op'>)</span>, - data <span class='op'>=</span> <span class='va'>d_syn</span>, na.action <span class='op'>=</span> <span class='va'>na.omit</span>, - start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, lrc <span class='op'>=</span> <span class='op'>-</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> -<span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> - <span class='va'>f_gnls_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls</span>, weights <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/varConstProp.html'>varConstProp</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> - <span class='va'>f_gnls_tc_sf</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_gnls_tc</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>sigma <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> -<span class='op'>}</span> -<span class='va'>f_mkin</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"const"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>f_mkin_tc</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='va'>d_syn</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='plot.mkinfit.html'>plot_res</a></span><span class='op'>(</span><span class='va'>f_mkin_tc</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='img'><img src='sigma_twocomp-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span><span class='op'>(</span><span class='va'>f_nls</span>, <span class='va'>f_gnls</span>, <span class='va'>f_gnls_tc</span>, <span class='va'>f_gnls_tc_sf</span>, <span class='va'>f_mkin</span>, <span class='va'>f_mkin_tc</span><span class='op'>)</span> -</div><div class='output co'>#> df AIC -#> f_nls 3 114.4817 -#> f_gnls 3 114.4817 -#> f_gnls_tc 5 103.6447 -#> f_gnls_tc_sf 4 101.6447 -#> f_mkin 3 114.4817 -#> f_mkin_tc 4 101.6446</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">times</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_pred</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">d_syn</span> <span class="op"><-</span> <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_pred</span>, <span class="kw">function</span><span class="op">(</span><span class="va">y</span><span class="op">)</span> <span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="fl">1</span>, <span class="fl">0.07</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> reps <span class="op">=</span> <span class="fl">2</span>, n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span></span> +<span class="r-in"><span><span class="va">f_nls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>, data <span class="op">=</span> <span class="va">d_syn</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_gnls</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/gnls.html" class="external-link">gnls</a></span><span class="op">(</span><span class="va">value</span> <span class="op">~</span> <span class="fu"><a href="https://rdrr.io/r/stats/SSasymp.html" class="external-link">SSasymp</a></span><span class="op">(</span><span class="va">time</span>, <span class="fl">0</span>, <span class="va">parent_0</span>, <span class="va">lrc</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> data <span class="op">=</span> <span class="va">d_syn</span>, na.action <span class="op">=</span> <span class="va">na.omit</span>,</span></span> +<span class="r-in"><span> start <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>parent_0 <span class="op">=</span> <span class="fl">100</span>, lrc <span class="op">=</span> <span class="op">-</span><span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="fu">findFunction</span><span class="op">(</span><span class="st">"varConstProp"</span><span class="op">)</span><span class="op">)</span> <span class="op">></span> <span class="fl">0</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls</span>, weights <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/varConstProp.html" class="external-link">varConstProp</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="va">f_gnls_tc_sf</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_gnls_tc</span>, control <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>sigma <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span><span class="va">f_mkin</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"const"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">f_mkin_tc</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">d_syn</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_res</a></span><span class="op">(</span><span class="va">f_mkin_tc</span>, standardized <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="sigma_twocomp-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">f_nls</span>, <span class="va">f_gnls</span>, <span class="va">f_gnls_tc</span>, <span class="va">f_gnls_tc_sf</span>, <span class="va">f_mkin</span>, <span class="va">f_mkin_tc</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> df AIC</span> +<span class="r-out co"><span class="r-pr">#></span> f_nls 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls_tc 5 103.6447</span> +<span class="r-out co"><span class="r-pr">#></span> f_gnls_tc_sf 4 101.6447</span> +<span class="r-out co"><span class="r-pr">#></span> f_mkin 3 114.4817</span> +<span class="r-out co"><span class="r-pr">#></span> f_mkin_tc 4 101.6446</span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index 4c856100..c3516f07 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -59,7 +59,10 @@ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index 3994a424..ad8432bf 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -211,10 +214,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Nov 14 21:06:31 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Nov 14 21:06:31 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:06 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:06 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index 96c2d0e5..0c0248fb 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -132,7 +135,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.767 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.842 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index 067efcfe..dcf2bd3d 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.1.2</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -48,19 +48,25 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -229,11 +235,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.158 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.1.2 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 10 15:27:32 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 10 15:27:32 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.160 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:11 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:11 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -243,7 +249,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.534 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.542 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index d8a41356..a4150959 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -63,7 +63,10 @@ endpoints such as formation fractions and DT50 values. Optionally <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -243,26 +246,26 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 828.1 822.7 -400.1</span> +<span class="r-out co"><span class="r-pr">#></span> 810.8 805.4 -391.4</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fitted parameters:</span> -<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.74378 97.81291 103.67465</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06168 -4.17104 -3.95231</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92584 -1.31273 -0.53894</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.81914 -3.60206 -2.03623</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63916 -4.32672 -2.95161</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02927 -1.15247 1.09394</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.86164 0.67928 1.04400</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.07973 0.06437 0.09509</span> -<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.73313 -7.46512 8.93137</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.06488 -0.06041 0.19017</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.41955 0.15206 0.68705</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.81750 0.29140 1.34361</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75265 0.27939 1.22590</span> -<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.34411 -1.70964 2.39786</span> +<span class="r-out co"><span class="r-pr">#></span> estimate lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.86947 97.81542 103.92353</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06947 -4.16944 -3.96950</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.93256 -1.34200 -0.52312</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.37017 -2.72660 -2.01375</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.06264 -4.21344 -3.91184</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.02174 -0.45898 0.41549</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.87598 0.67275 1.07922</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.07949 0.06389 0.09509</span> +<span class="r-out co"><span class="r-pr">#></span> SD.parent_0 0.19170 -30.36286 30.74626</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k_m1 0.01883 -0.28736 0.32502</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44300 0.16391 0.72209</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35320 0.09661 0.60978</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.13707 0.02359 0.25056</span> +<span class="r-out co"><span class="r-pr">#></span> SD.g_qlogis 0.37478 0.04490 0.70467</span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)" "sd(g_qlogis)"</span> +<span class="r-out co"><span class="r-pr">#></span> [1] "sd(parent_0)" "sd(log_k_m1)"</span> <span class="r-in"><span><span class="va">f_saem_dfop_sfo_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, covariance.model <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/diag.html" class="external-link">diag</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">1</span>, <span class="fl">0</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span><span class="op">)</span></span></span> @@ -270,29 +273,29 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Fixed effects:</span> <span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 97.54844979 100.46239264 103.37633550</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01575805 0.01729111 0.01897331</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.21014925 0.28626877 0.37680664</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.02651112 0.05601399 0.11834908</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.01326524 0.02649799 0.05293107</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.31467778 0.51297098 0.70726363</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 97.57609542 100.73343868 103.89078195</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01549292 0.01714893 0.01898194</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.20720315 0.28358738 0.37481744</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.06149334 0.08733164 0.12402670</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01448390 0.01699942 0.01995184</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.45084762 0.51075839 0.57036168</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.1658367 0.4471180 0.7283993</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.2768757 0.7929203 1.3089649</span> -<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.2693629 0.7566116 1.2438602</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> sd(f_parent_qlogis) 0.16606767 0.4479731 0.7298784</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k1) 0.12284609 0.3588446 0.5948430</span> +<span class="r-out co"><span class="r-pr">#></span> sd(log_k2) 0.05379723 0.1548780 0.2559588</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.70273100 0.88750764 1.07228428</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.06781347 0.08328016 0.09874685</span> +<span class="r-out co"><span class="r-pr">#></span> lower est. upper</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.6811490 0.88503409 1.08891921</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.0676515 0.08336272 0.09907394</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.0 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.2 </span> <span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Tue Nov 1 14:12:50 2022 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Tue Nov 1 14:12:50 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:52 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:52 2022 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -307,7 +310,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 25.006 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 26.242 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> @@ -325,233 +328,233 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Likelihood computed by importance sampling</span> <span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> -<span class="r-out co"><span class="r-pr">#></span> 825.6 821.3 -401.8</span> +<span class="r-out co"><span class="r-pr">#></span> 809.5 805.2 -393.7</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Optimised parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.05756 -4.15040 -3.96472</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.91358 -1.32403 -0.50312</span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.88215 -3.63019 -2.13412</span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -3.63069 -4.32261 -2.93876</span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.05190 -0.77834 0.88213</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44712 0.16584 0.72840</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.79292 0.27688 1.30896</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.75661 0.26936 1.24386</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.06582 -4.16737 -3.96427</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.92674 -1.34187 -0.51160</span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 -2.43804 -2.78883 -2.08726</span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -4.07458 -4.23472 -3.91443</span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.04304 -0.19725 0.28333</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.44797 0.16607 0.72988</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.35884 0.12285 0.59484</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.15488 0.05380 0.25596</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Correlation: </span> <span class="r-out co"><span class="r-pr">#></span> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4102 </span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2113 0.2439 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1308 -0.1305 -0.0504 </span> -<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0383 0.0592 0.0151 0.0001 </span> -<span class="r-out co"><span class="r-pr">#></span> g_qlogis -0.0029 -0.0118 0.0131 -0.2547 -0.1942</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -0.4698 </span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -0.2461 0.2709 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k1 0.1572 -0.1517 -0.0648 </span> +<span class="r-out co"><span class="r-pr">#></span> log_k2 -0.0023 0.0835 0.0125 0.1420 </span> +<span class="r-out co"><span class="r-pr">#></span> g_qlogis 0.2314 -0.2337 -0.0755 -0.2762 -0.4797</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Random effects:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4471 0.1658 0.7284</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.7929 0.2769 1.3090</span> -<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.7566 0.2694 1.2439</span> +<span class="r-out co"><span class="r-pr">#></span> SD.f_parent_qlogis 0.4480 0.1661 0.7299</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k1 0.3588 0.1228 0.5948</span> +<span class="r-out co"><span class="r-pr">#></span> SD.log_k2 0.1549 0.0538 0.2560</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> a.1 0.88751 0.70273 1.07228</span> -<span class="r-out co"><span class="r-pr">#></span> b.1 0.08328 0.06781 0.09875</span> +<span class="r-out co"><span class="r-pr">#></span> a.1 0.88503 0.68115 1.08892</span> +<span class="r-out co"><span class="r-pr">#></span> b.1 0.08336 0.06765 0.09907</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> <span class="r-out co"><span class="r-pr">#></span> est. lower upper</span> -<span class="r-out co"><span class="r-pr">#></span> parent_0 100.46239 97.54845 103.37634</span> -<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01729 0.01576 0.01897</span> -<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28627 0.21015 0.37681</span> -<span class="r-out co"><span class="r-pr">#></span> k1 0.05601 0.02651 0.11835</span> -<span class="r-out co"><span class="r-pr">#></span> k2 0.02650 0.01327 0.05293</span> -<span class="r-out co"><span class="r-pr">#></span> g 0.51297 0.31468 0.70726</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 100.73344 97.57610 103.89078</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.01715 0.01549 0.01898</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.28359 0.20720 0.37482</span> +<span class="r-out co"><span class="r-pr">#></span> k1 0.08733 0.06149 0.12403</span> +<span class="r-out co"><span class="r-pr">#></span> k2 0.01700 0.01448 0.01995</span> +<span class="r-out co"><span class="r-pr">#></span> g 0.51076 0.45085 0.57036</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> <span class="r-out co"><span class="r-pr">#></span> ff</span> -<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2863</span> -<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7137</span> +<span class="r-out co"><span class="r-pr">#></span> parent_m1 0.2836</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.7164</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> <span class="r-out co"><span class="r-pr">#></span> DT50 DT90 DT50back DT50_k1 DT50_k2</span> -<span class="r-out co"><span class="r-pr">#></span> parent 17.44 65.15 19.61 12.37 26.16</span> -<span class="r-out co"><span class="r-pr">#></span> m1 40.09 133.17 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> parent 15.94 93.48 28.14 7.937 40.77</span> +<span class="r-out co"><span class="r-pr">#></span> m1 40.42 134.27 NA NA NA</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Data:</span> -<span class="r-out co"><span class="r-pr">#></span> ds name time observed predicted residual std standardized</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 89.8 1.005e+02 -10.662393 8.4135 -1.267301</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 0 104.1 1.005e+02 3.637607 8.4135 0.432355</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 88.7 9.576e+01 -7.063498 8.0244 -0.880249</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 1 95.5 9.576e+01 -0.263498 8.0244 -0.032837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 81.8 8.717e+01 -5.369491 7.3135 -0.734185</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 3 94.5 8.717e+01 7.330509 7.3135 1.002320</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.274e+01 -1.238672 6.1224 -0.202319</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.274e+01 -2.438672 6.1224 -0.398322</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.418e+01 0.022691 4.5984 0.004935</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.418e+01 -4.577309 4.5984 -0.995423</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.241e+01 -0.914545 2.8416 -0.321837</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.241e+01 -3.614545 2.8416 -1.271993</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.283e+01 -0.730904 1.3891 -0.526186</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.283e+01 0.769096 1.3891 0.553681</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.128e+00 0.071981 1.0238 0.070309</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.128e+00 2.171981 1.0238 2.121538</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.022e+00 -0.822164 0.9225 -0.891230</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.022e+00 -0.622164 0.9225 -0.674429</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.163e+00 -0.863423 0.8928 -0.967116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.163e+00 -0.963423 0.8928 -1.079126</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.233e+00 -1.032930 0.9274 -1.113734</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.233e+00 -0.232930 0.9274 -0.251152</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.495e+00 0.005314 1.0393 0.005113</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.495e+00 -1.494686 1.0393 -1.438116</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.010e+01 0.096372 1.2230 0.078801</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.010e+01 -0.603628 1.2230 -0.493572</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.269e+01 -0.492073 1.3802 -0.356526</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.269e+01 0.707927 1.3802 0.512922</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.086e+01 0.944360 1.2669 0.745420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.086e+01 2.344360 1.2669 1.850494</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.723e+00 -1.123088 1.0961 -1.024658</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.723e+00 1.576912 1.0961 1.438708</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.184e+00 -1.683936 0.9869 -1.706219</span> -<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.184e+00 0.216064 0.9869 0.218923</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.005e+02 17.537607 8.4135 2.084469</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.005e+02 -0.662393 8.4135 -0.078730</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.566e+01 -5.456414 8.0156 -0.680727</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.566e+01 -1.056414 8.0156 -0.131795</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.702e+01 9.082833 7.3009 1.244062</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.702e+01 -8.617167 7.3009 -1.180281</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.298e+01 4.919834 6.1423 0.800981</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.298e+01 4.719834 6.1423 0.768420</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.588e+01 0.124003 4.7372 0.026176</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.588e+01 -1.175997 4.7372 -0.248245</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.719e+01 -0.587869 3.2217 -0.182474</span> -<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.719e+01 -0.387869 3.2217 -0.120394</span> -<span 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7.3159 1.00936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 71.5 7.246e+01 -0.95675 6.1047 -0.15672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 7 70.3 7.246e+01 -2.15675 6.1047 -0.35329</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 54.2 5.382e+01 0.38143 4.5729 0.08341</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 14 49.6 5.382e+01 -4.21857 4.5729 -0.92251</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 31.5 3.230e+01 -0.80120 2.8344 -0.28267</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 28 28.8 3.230e+01 -3.50120 2.8344 -1.23524</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 12.1 1.307e+01 -0.97165 1.4038 -0.69215</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 60 13.6 1.307e+01 0.52835 1.4038 0.37637</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 6.2 6.353e+00 -0.15285 1.0314 -0.14820</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 90 8.3 6.353e+00 1.94715 1.0314 1.88790</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.2 3.175e+00 -0.97462 0.9238 -1.05506</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 parent 120 2.4 3.175e+00 -0.77462 0.9238 -0.83855</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.3 1.183e+00 -0.88350 0.8905 -0.99212</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 1 0.2 1.183e+00 -0.98350 0.8905 -1.10441</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 2.2 3.281e+00 -1.08106 0.9263 -1.16703</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 3 3.0 3.281e+00 -0.28106 0.9263 -0.30341</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 6.5 6.564e+00 -0.06353 1.0405 -0.06106</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 7 5.0 6.564e+00 -1.56353 1.0405 -1.50266</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 10.2 1.015e+01 0.05147 1.2243 0.04204</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 14 9.5 1.015e+01 -0.64853 1.2243 -0.52970</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 12.2 1.265e+01 -0.44824 1.3766 -0.32561</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 28 13.4 1.265e+01 0.75176 1.3766 0.54610</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 11.8 1.078e+01 1.02355 1.2611 0.81165</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 60 13.2 1.078e+01 2.42355 1.2611 1.92181</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 6.6 7.698e+00 -1.09840 1.0932 -1.00474</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 90 9.3 7.698e+00 1.60160 1.0932 1.46502</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 3.5 5.199e+00 -1.69853 0.9854 -1.72363</span> +<span class="r-out co"><span class="r-pr">#></span> ds 1 m1 120 5.4 5.199e+00 0.20147 0.9854 0.20445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 118.0 1.007e+02 17.26656 8.4439 2.04485</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 0 99.8 1.007e+02 -0.93344 8.4439 -0.11055</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 90.2 9.584e+01 -5.63852 8.0382 -0.70146</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 1 94.6 9.584e+01 -1.23852 8.0382 -0.15408</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 96.1 8.706e+01 9.04068 7.3113 1.23654</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 3 78.4 8.706e+01 -8.65932 7.3113 -1.18438</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.9 7.286e+01 5.04438 6.1376 0.82188</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 7 77.7 7.286e+01 4.84438 6.1376 0.78930</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 56.0 5.567e+01 0.33336 4.7242 0.07057</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 14 54.7 5.567e+01 -0.96664 4.7242 -0.20462</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.6 3.705e+01 -0.44800 3.2127 -0.13944</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 28 36.8 3.705e+01 -0.24800 3.2127 -0.07719</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 22.1 2.008e+01 2.01984 1.8935 1.06672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 60 24.7 2.008e+01 4.61984 1.8935 2.43984</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 12.4 1.253e+01 -0.12814 1.3689 -0.09360</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 90 10.8 1.253e+01 -1.72814 1.3689 -1.26238</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 6.8 7.916e+00 -1.11595 1.1040 -1.01085</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 parent 120 7.9 7.916e+00 -0.01595 1.1040 -0.01445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 1 1.3 1.317e+00 -0.01669 0.8918 -0.01871</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 3.7 3.613e+00 0.08699 0.9349 0.09305</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 3 4.7 3.613e+00 1.08699 0.9349 1.16270</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 8.1 7.092e+00 1.00781 1.0643 0.94688</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 7 7.9 7.092e+00 0.80781 1.0643 0.75897</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.1 1.066e+01 -0.56458 1.2545 -0.45006</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 14 10.3 1.066e+01 -0.36458 1.2545 -0.29063</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 10.7 1.281e+01 -2.11106 1.3870 -1.52201</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 28 12.2 1.281e+01 -0.61106 1.3870 -0.44055</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 10.7 1.078e+01 -0.08464 1.2616 -0.06709</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 60 12.5 1.078e+01 1.71536 1.2616 1.35970</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 9.1 8.013e+00 1.08684 1.1088 0.98016</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 90 7.4 8.013e+00 -0.61316 1.1088 -0.55298</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 6.1 5.749e+00 0.35063 1.0065 0.34838</span> +<span class="r-out co"><span class="r-pr">#></span> ds 2 m1 120 4.5 5.749e+00 -1.24937 1.0065 -1.24133</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.2 1.007e+02 5.46656 8.4439 0.64740</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 0 106.9 1.007e+02 6.16656 8.4439 0.73030</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 107.4 9.369e+01 13.70530 7.8606 1.74354</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 1 96.1 9.369e+01 2.40530 7.8606 0.30599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 79.4 8.185e+01 -2.45363 6.8807 -0.35660</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 3 82.6 8.185e+01 0.74637 6.8807 0.10847</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 63.9 6.487e+01 -0.97153 5.4798 -0.17729</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 7 62.4 6.487e+01 -2.47153 5.4798 -0.45103</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 51.0 4.791e+01 3.09024 4.0908 0.75542</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 14 47.1 4.791e+01 -0.80976 4.0908 -0.19795</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.1 3.313e+01 2.97112 2.9001 1.02450</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 28 36.6 3.313e+01 3.47112 2.9001 1.19691</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 20.1 1.927e+01 0.83265 1.8339 0.45404</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 60 19.8 1.927e+01 0.53265 1.8339 0.29045</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 11.3 1.203e+01 -0.72783 1.3374 -0.54421</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 90 10.7 1.203e+01 -1.32783 1.3374 -0.99284</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 8.2 7.516e+00 0.68382 1.0844 0.63061</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 parent 120 7.3 7.516e+00 -0.21618 1.0844 -0.19936</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 0 0.8 -9.948e-14 0.80000 0.8850 0.90392</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 1.8 1.682e+00 0.11759 0.8961 0.13123</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 1 2.3 1.682e+00 0.61759 0.8961 0.68921</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.2 4.431e+00 -0.23052 0.9590 -0.24037</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 3 4.1 4.431e+00 -0.33052 0.9590 -0.34465</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 6.8 8.084e+00 -1.28422 1.1124 -1.15445</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 7 10.1 8.084e+00 2.01578 1.1124 1.81208</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 11.4 1.100e+01 0.40274 1.2743 0.31606</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 14 12.8 1.100e+01 1.80274 1.2743 1.41474</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 11.5 1.176e+01 -0.25977 1.3207 -0.19669</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 28 10.6 1.176e+01 -1.15977 1.3207 -0.87813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 7.5 9.277e+00 -1.77696 1.1753 -1.51190</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 60 8.6 9.277e+00 -0.67696 1.1753 -0.57598</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 7.3 6.883e+00 0.41708 1.0548 0.39542</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 90 8.1 6.883e+00 1.21708 1.0548 1.15389</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 5.3 4.948e+00 0.35179 0.9764 0.36028</span> +<span class="r-out co"><span class="r-pr">#></span> ds 3 m1 120 3.8 4.948e+00 -1.14821 0.9764 -1.17591</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 104.7 1.007e+02 3.96656 8.4439 0.46975</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 0 88.3 1.007e+02 -12.43344 8.4439 -1.47247</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.2 9.738e+01 -3.18358 8.1663 -0.38985</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 1 94.6 9.738e+01 -2.78358 8.1663 -0.34086</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 78.1 9.110e+01 -12.99595 7.6454 -1.69984</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 3 96.5 9.110e+01 5.40405 7.6454 0.70684</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 76.2 8.000e+01 -3.79797 6.7273 -0.56456</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 7 77.8 8.000e+01 -2.19797 6.7273 -0.32672</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 70.8 6.446e+01 6.34396 5.4456 1.16496</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 14 67.3 6.446e+01 2.84396 5.4456 0.52225</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 43.1 4.359e+01 -0.48960 3.7400 -0.13091</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 28 45.1 4.359e+01 1.51040 3.7400 0.40385</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 21.3 2.095e+01 0.35282 1.9577 0.18022</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 60 23.5 2.095e+01 2.55282 1.9577 1.30400</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 11.8 1.188e+01 -0.07874 1.3281 -0.05929</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 90 12.1 1.188e+01 0.22126 1.3281 0.16660</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 7.0 7.072e+00 -0.07245 1.0634 -0.06813</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 parent 120 6.2 7.072e+00 -0.87245 1.0634 -0.82041</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 0 1.6 5.684e-14 1.60000 0.8850 1.80784</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 1 0.9 6.960e-01 0.20399 0.8869 0.23000</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 3.7 1.968e+00 1.73240 0.9001 1.92466</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 3 2.0 1.968e+00 0.03240 0.9001 0.03599</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.6 4.083e+00 -0.48287 0.9482 -0.50924</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 7 3.8 4.083e+00 -0.28287 0.9482 -0.29832</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 7.1 6.682e+00 0.41836 1.0457 0.40007</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 14 6.6 6.682e+00 -0.08164 1.0457 -0.07807</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.5 9.103e+00 0.39733 1.1658 0.34082</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 28 9.3 9.103e+00 0.19733 1.1658 0.16926</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 8.3 8.750e+00 -0.44979 1.1469 -0.39218</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 60 9.0 8.750e+00 0.25021 1.1469 0.21817</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 6.6 6.673e+00 -0.07285 1.0453 -0.06969</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 90 7.7 6.673e+00 1.02715 1.0453 0.98261</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.7 4.757e+00 -1.05747 0.9698 -1.09036</span> +<span class="r-out co"><span class="r-pr">#></span> ds 4 m1 120 3.5 4.757e+00 -1.25747 0.9698 -1.29658</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 110.4 1.007e+02 9.66656 8.4439 1.14480</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 0 112.1 1.007e+02 11.36656 8.4439 1.34612</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 93.5 9.395e+01 -0.45394 7.8821 -0.05759</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 1 91.0 9.395e+01 -2.95394 7.8821 -0.37477</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 71.0 8.245e+01 -11.44783 6.9298 -1.65197</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 3 89.7 8.245e+01 7.25217 6.9298 1.04652</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 60.4 6.567e+01 -5.27002 5.5455 -0.95032</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 7 59.1 6.567e+01 -6.57002 5.5455 -1.18475</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 56.5 4.847e+01 8.03029 4.1364 1.94139</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 14 47.0 4.847e+01 -1.46971 4.1364 -0.35532</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 30.2 3.309e+01 -2.89206 2.8971 -0.99825</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 28 23.9 3.309e+01 -9.19206 2.8971 -3.17281</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 17.0 1.891e+01 -1.90623 1.8076 -1.05458</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 60 18.7 1.891e+01 -0.20623 1.8076 -0.11409</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.3 1.168e+01 -0.38263 1.3160 -0.29076</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 90 11.9 1.168e+01 0.21737 1.3160 0.16518</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 9.0 7.230e+00 1.77031 1.0708 1.65333</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 parent 120 8.1 7.230e+00 0.87031 1.0708 0.81280</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 0 0.7 -5.116e-13 0.70000 0.8850 0.79093</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 3.0 3.244e+00 -0.24430 0.9254 -0.26398</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 1 2.6 3.244e+00 -0.64430 0.9254 -0.69621</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 5.1 8.592e+00 -3.49175 1.1385 -3.06686</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 3 7.5 8.592e+00 -1.09175 1.1385 -0.95890</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 16.5 1.583e+01 0.66887 1.5890 0.42093</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 7 19.0 1.583e+01 3.16887 1.5890 1.99424</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 22.9 2.181e+01 1.08658 2.0224 0.53728</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 14 23.2 2.181e+01 1.38658 2.0224 0.68562</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 22.2 2.364e+01 -1.43659 2.1600 -0.66508</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 28 24.4 2.364e+01 0.76341 2.1600 0.35342</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 15.5 1.873e+01 -3.23377 1.7950 -1.80150</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 60 19.8 1.873e+01 1.06623 1.7950 0.59398</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.9 1.387e+01 1.03117 1.4560 0.70822</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 90 14.2 1.387e+01 0.33117 1.4560 0.22745</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.9 9.937e+00 0.96270 1.2122 0.79415</span> +<span class="r-out co"><span class="r-pr">#></span> ds 5 m1 120 10.4 9.937e+00 0.46270 1.2122 0.38169</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> </code></pre></div> diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png Binary files differindex 89975db5..132380a8 100644 --- a/docs/dev/reference/synthetic_data_for_UBA_2014-1.png +++ b/docs/dev/reference/synthetic_data_for_UBA_2014-1.png diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014"><meta property="og:description" content="The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites. Variance component 'a' is based on a normal distribution with standard deviation of 3, @@ -55,28 +14,14 @@ Initial concentrations for metabolites and all values where adding the variance in a value below the assumed limit of detection of 0.1 were set to NA. As an example, the first dataset has the title SFO_lin_a and is based on the SFO model with two sequential metabolites (linear pathway), with added variance component 'a'. -Compare also the code in the example section to see the degradation models." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +Compare also the code in the example section to see the degradation models."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -87,23 +32,21 @@ Compare also the code in the example section to see the degradation models." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -113,44 +56,46 @@ Compare also the code in the example section to see the degradation models." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Synthetic datasets for one parent compound with two metabolites</h1> @@ -177,300 +122,308 @@ Compare also the code in the example section to see the degradation models." /> <p>Compare also the code in the example section to see the degradation models.</p> </div> - <pre class="usage"><span class='va'>synthetic_data_for_UBA_2014</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">synthetic_data_for_UBA_2014</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, + each containing, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='co'># The data have been generated using the following kinetic models</span> -<span class='va'>m_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - -<span class='va'>m_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_DFOP_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='st'>"M1"</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"M2"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>m_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"DFOP"</span>, to <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span>, - sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># The model predictions without intentional error were generated as follows</span> -<span class='va'>sampling_times</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span><span class='op'>)</span> - -<span class='va'>d_synth_SFO_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.7</span>, f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>, - k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>, f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>, - k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_DFOP_lin</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_lin</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.2</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.5</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.5</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.3</span>, - f_M1_to_M2 <span class='op'>=</span> <span class='fl'>0.7</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_SFO_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_par</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.2</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.8</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.01</span>, - f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.2</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.02</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='va'>d_synth_DFOP_par</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_synth_DFOP_par</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k1 <span class='op'>=</span> <span class='fl'>0.3</span>, k2 <span class='op'>=</span> <span class='fl'>0.02</span>, g <span class='op'>=</span> <span class='fl'>0.7</span>, - f_parent_to_M1 <span class='op'>=</span> <span class='fl'>0.6</span>, k_M1 <span class='op'>=</span> <span class='fl'>0.04</span>, - f_parent_to_M2 <span class='op'>=</span> <span class='fl'>0.4</span>, k_M2 <span class='op'>=</span> <span class='fl'>0.01</span><span class='op'>)</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span>, M1 <span class='op'>=</span> <span class='fl'>0</span>, M2 <span class='op'>=</span> <span class='fl'>0</span><span class='op'>)</span>, - <span class='va'>sampling_times</span><span class='op'>)</span> - -<span class='co'># Construct names for datasets with errors</span> -<span class='va'>d_synth_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"d_synth_"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO_lin"</span>, <span class='st'>"SFO_par"</span>, - <span class='st'>"DFOP_lin"</span>, <span class='st'>"DFOP_par"</span><span class='op'>)</span><span class='op'>)</span> - -<span class='co'># Original function used or adding errors. The add_err function now published</span> -<span class='co'># with this package is a slightly generalised version where the names of</span> -<span class='co'># secondary compartments that should have an initial value of zero (M1 and M2</span> -<span class='co'># in this case) are not hardcoded any more.</span> -<span class='co'># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span> -<span class='co'># {</span> -<span class='co'># set.seed(seed)</span> -<span class='co'># d_long = mkin_wide_to_long(d, time = "time")</span> -<span class='co'># d_rep = data.frame(lapply(d_long, rep, each = 2))</span> -<span class='co'># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span> -<span class='co'>#</span> -<span class='co'># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span> -<span class='co'># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span> -<span class='co'># d_NA$value <- round(d_NA$value, 1)</span> -<span class='co'># return(d_NA)</span> -<span class='co'># }</span> - -<span class='co'># The following is the simplified version of the two-component model of Rocke</span> -<span class='co'># and Lorenzato (1995)</span> -<span class='va'>sdfunc_twocomp</span> <span class='op'>=</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span>, <span class='va'>sd_low</span>, <span class='va'>rsd_high</span><span class='op'>)</span> <span class='op'>{</span> - <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>sqrt</a></span><span class='op'>(</span><span class='va'>sd_low</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>+</span> <span class='va'>value</span><span class='op'>^</span><span class='fl'>2</span> <span class='op'>*</span> <span class='va'>rsd_high</span><span class='op'>^</span><span class='fl'>2</span><span class='op'>)</span> -<span class='op'>}</span> - -<span class='co'># Add the errors.</span> -<span class='kw'>for</span> <span class='op'>(</span><span class='va'>d_synth_name</span> <span class='kw'>in</span> <span class='va'>d_synth_names</span><span class='op'>)</span> -<span class='op'>{</span> - <span class='va'>d_synth</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/get.html'>get</a></span><span class='op'>(</span><span class='va'>d_synth_name</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_a"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_b"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>7</span><span class='op'>)</span><span class='op'>)</span> - <span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>d_synth_name</span>, <span class='st'>"_c"</span><span class='op'>)</span>, <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_synth</span>, - <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fu'>sdfunc_twocomp</span><span class='op'>(</span><span class='va'>value</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> - -<span class='op'>}</span> - -<span class='va'>d_synth_err_names</span> <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span> - <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/rep.html'>rep</a></span><span class='op'>(</span><span class='va'>d_synth_names</span>, each <span class='op'>=</span> <span class='fl'>3</span><span class='op'>)</span>, <span class='va'>letters</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>3</span><span class='op'>]</span>, sep <span class='op'>=</span> <span class='st'>"_"</span><span class='op'>)</span> -<span class='op'>)</span> - -<span class='co'># This is just one example of an evaluation using the kinetic model used for</span> -<span class='co'># the generation of the data</span> - <span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_synth_SFO_lin</span>, <span class='va'>synthetic_data_for_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, - quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> - <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> mkin version used for fitting: 1.0.3.9000 -#> R version used for fitting: 4.0.3 -#> Date of fit: Mon Feb 15 17:13:29 2021 -#> Date of summary: Mon Feb 15 17:13:29 2021 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 -#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2 -#> -#> Model predictions using solution type deSolve -#> -#> Fitted using 833 model solutions performed in 0.649 s -#> -#> Error model: Constant variance -#> -#> Error model algorithm: OLS -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.3500 state -#> k_parent 0.1000 deparm -#> k_M1 0.1001 deparm -#> k_M2 0.1002 deparm -#> f_parent_to_M1 0.5000 deparm -#> f_M1_to_M2 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 101.350000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_M1 -2.301586 -Inf Inf -#> log_k_M2 -2.300587 -Inf Inf -#> f_parent_qlogis 0.000000 -Inf Inf -#> f_M1_qlogis 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> M1_0 0 state -#> M2_0 0 state -#> -#> Results: -#> -#> AIC BIC logLik -#> 188.7274 200.3723 -87.36368 -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 102.1000 1.57000 98.8600 105.3000 -#> log_k_parent -0.3020 0.03885 -0.3812 -0.2229 -#> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620 -#> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670 -#> f_parent_qlogis 1.2010 0.23530 0.7216 1.6800 -#> f_M1_qlogis 0.9589 0.24890 0.4520 1.4660 -#> sigma 2.2730 0.25740 1.7490 2.7970 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_qlogis -#> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01 -#> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01 -#> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01 -#> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 -#> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 -#> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 -#> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08 -#> f_M1_qlogis sigma -#> parent_0 1.614e-01 -2.900e-08 -#> log_k_parent 4.102e-01 -8.030e-09 -#> log_k_M1 -8.109e-01 -2.741e-08 -#> log_k_M2 5.419e-01 3.938e-08 -#> f_parent_qlogis -8.605e-01 -2.681e-08 -#> f_M1_qlogis 1.000e+00 4.971e-08 -#> sigma 4.971e-08 1.000e+00 -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000 -#> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020 -#> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590 -#> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312 -#> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290 -#> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240 -#> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700 -#> -#> FOCUS Chi2 error levels in percent: -#> err.min n.optim df -#> All data 8.454 6 17 -#> parent 8.660 2 6 -#> M1 10.583 2 5 -#> M2 3.586 2 6 -#> -#> Resulting formation fractions: -#> ff -#> parent_M1 0.7687 -#> parent_sink 0.2313 -#> M1_M2 0.7229 -#> M1_sink 0.2771 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 0.9376 3.114 -#> M1 2.3170 7.697 -#> M2 34.2689 113.839 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 101.5 1.021e+02 -0.56248 -#> 0 parent 101.2 1.021e+02 -0.86248 -#> 1 parent 53.9 4.873e+01 5.17118 -#> 1 parent 47.5 4.873e+01 -1.22882 -#> 3 parent 10.4 1.111e+01 -0.70773 -#> 3 parent 7.6 1.111e+01 -3.50773 -#> 7 parent 1.1 5.772e-01 0.52283 -#> 7 parent 0.3 5.772e-01 -0.27717 -#> 14 parent 3.5 3.264e-03 3.49674 -#> 28 parent 3.2 1.045e-07 3.20000 -#> 90 parent 0.6 9.530e-10 0.60000 -#> 120 parent 3.5 -5.940e-10 3.50000 -#> 1 M1 36.4 3.479e+01 1.61088 -#> 1 M1 37.4 3.479e+01 2.61088 -#> 3 M1 34.3 3.937e+01 -5.07027 -#> 3 M1 39.8 3.937e+01 0.42973 -#> 7 M1 15.1 1.549e+01 -0.38715 -#> 7 M1 17.8 1.549e+01 2.31285 -#> 14 M1 5.8 1.995e+00 3.80469 -#> 14 M1 1.2 1.995e+00 -0.79531 -#> 60 M1 0.5 2.111e-06 0.50000 -#> 90 M1 3.2 -9.670e-10 3.20000 -#> 120 M1 1.5 7.670e-10 1.50000 -#> 120 M1 0.6 7.670e-10 0.60000 -#> 1 M2 4.8 4.455e+00 0.34517 -#> 3 M2 20.9 2.153e+01 -0.62527 -#> 3 M2 19.3 2.153e+01 -2.22527 -#> 7 M2 42.0 4.192e+01 0.07941 -#> 7 M2 43.1 4.192e+01 1.17941 -#> 14 M2 49.4 4.557e+01 3.83353 -#> 14 M2 44.3 4.557e+01 -1.26647 -#> 28 M2 34.6 3.547e+01 -0.87275 -#> 28 M2 33.0 3.547e+01 -2.47275 -#> 60 M2 18.8 1.858e+01 0.21837 -#> 60 M2 17.6 1.858e+01 -0.98163 -#> 90 M2 10.6 1.013e+01 0.47130 -#> 90 M2 10.8 1.013e+01 0.67130 -#> 120 M2 9.8 5.521e+00 4.27893 -#> 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'><span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The data have been generated using the following kinetic models</span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">m_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"DFOP"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The model predictions without intentional error were generated as follows</span></span></span> +<span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.7</span>, f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>,</span></span> +<span class="r-in"><span> k_M1 <span class="op">=</span> <span class="fl">0.3</span>, f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_lin</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.2</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.5</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.5</span>, k_M1 <span class="op">=</span> <span class="fl">0.3</span>,</span></span> +<span class="r-in"><span> f_M1_to_M2 <span class="op">=</span> <span class="fl">0.7</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_SFO_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_SFO_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.2</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.8</span>, k_M1 <span class="op">=</span> <span class="fl">0.01</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.2</span>, k_M2 <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_DFOP_par</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_synth_DFOP_par</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="fl">0.3</span>, k2 <span class="op">=</span> <span class="fl">0.02</span>, g <span class="op">=</span> <span class="fl">0.7</span>,</span></span> +<span class="r-in"><span> f_parent_to_M1 <span class="op">=</span> <span class="fl">0.6</span>, k_M1 <span class="op">=</span> <span class="fl">0.04</span>,</span></span> +<span class="r-in"><span> f_parent_to_M2 <span class="op">=</span> <span class="fl">0.4</span>, k_M2 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, M1 <span class="op">=</span> <span class="fl">0</span>, M2 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="va">sampling_times</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Construct names for datasets with errors</span></span></span> +<span class="r-in"><span><span class="va">d_synth_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"d_synth_"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO_lin"</span>, <span class="st">"SFO_par"</span>,</span></span> +<span class="r-in"><span> <span class="st">"DFOP_lin"</span>, <span class="st">"DFOP_par"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Original function used or adding errors. The add_err function now published</span></span></span> +<span class="r-in"><span><span class="co"># with this package is a slightly generalised version where the names of</span></span></span> +<span class="r-in"><span><span class="co"># secondary compartments that should have an initial value of zero (M1 and M2</span></span></span> +<span class="r-in"><span><span class="co"># in this case) are not hardcoded any more.</span></span></span> +<span class="r-in"><span><span class="co"># add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)</span></span></span> +<span class="r-in"><span><span class="co"># {</span></span></span> +<span class="r-in"><span><span class="co"># set.seed(seed)</span></span></span> +<span class="r-in"><span><span class="co"># d_long = mkin_wide_to_long(d, time = "time")</span></span></span> +<span class="r-in"><span><span class="co"># d_rep = data.frame(lapply(d_long, rep, each = 2))</span></span></span> +<span class="r-in"><span><span class="co"># d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))</span></span></span> +<span class="r-in"><span><span class="co">#</span></span></span> +<span class="r-in"><span><span class="co"># d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0</span></span></span> +<span class="r-in"><span><span class="co"># d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))</span></span></span> +<span class="r-in"><span><span class="co"># d_NA$value <- round(d_NA$value, 1)</span></span></span> +<span class="r-in"><span><span class="co"># return(d_NA)</span></span></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># The following is the simplified version of the two-component model of Rocke</span></span></span> +<span class="r-in"><span><span class="co"># and Lorenzato (1995)</span></span></span> +<span class="r-in"><span><span class="va">sdfunc_twocomp</span> <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span>, <span class="va">sd_low</span>, <span class="va">rsd_high</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="va">sd_low</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="va">rsd_high</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Add the errors.</span></span></span> +<span class="r-in"><span><span class="kw">for</span> <span class="op">(</span><span class="va">d_synth_name</span> <span class="kw">in</span> <span class="va">d_synth_names</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">{</span></span></span> +<span class="r-in"><span> <span class="va">d_synth</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/get.html" class="external-link">get</a></span><span class="op">(</span><span class="va">d_synth_name</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_a"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">3</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_b"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>, <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/assign.html" class="external-link">assign</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="va">d_synth_name</span>, <span class="st">"_c"</span><span class="op">)</span>, <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">d_synth</span>,</span></span> +<span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu">sdfunc_twocomp</span><span class="op">(</span><span class="va">value</span>, <span class="fl">0.5</span>, <span class="fl">0.07</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="op">}</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">d_synth_err_names</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="va">d_synth_names</span>, each <span class="op">=</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">letters</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">]</span>, sep <span class="op">=</span> <span class="st">"_"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># This is just one example of an evaluation using the kinetic model used for</span></span></span> +<span class="r-in"><span><span class="co"># the generation of the data</span></span></span> +<span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_synth_SFO_lin</span>, <span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>,</span></span> +<span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 24 08:11:54 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 24 08:11:54 2022 </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Equations:</span> +<span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> +<span class="r-out co"><span class="r-pr">#></span> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1</span> +<span class="r-out co"><span class="r-pr">#></span> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.574 s</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Error model algorithm: OLS </span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for parameters to be optimised:</span> +<span class="r-out co"><span class="r-pr">#></span> value type</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.3500 state</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.1000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.1001 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.1002 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.5000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M2 0.5000 deparm</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Starting values for the transformed parameters actually optimised:</span> +<span class="r-out co"><span class="r-pr">#></span> value lower upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 101.350000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.302585 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -2.301586 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 -2.300587 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.000000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 0.000000 -Inf Inf</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Fixed parameter values:</span> +<span class="r-out co"><span class="r-pr">#></span> value type</span> +<span class="r-out co"><span class="r-pr">#></span> M1_0 0 state</span> +<span class="r-out co"><span class="r-pr">#></span> M2_0 0 state</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Results:</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> AIC BIC logLik</span> +<span class="r-out co"><span class="r-pr">#></span> 188.7274 200.3723 -87.36368</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Optimised, transformed parameters with symmetric confidence intervals:</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 102.1000 1.57000 98.8600 105.3000</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -0.3020 0.03885 -0.3812 -0.2229</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 1.2010 0.23530 0.7216 1.6800</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 0.9589 0.24890 0.4520 1.4660</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.2730 0.25740 1.7490 2.7970</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Parameter correlation:</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_qlogis</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01</span> +<span class="r-out co"><span class="r-pr">#></span> sigma -2.900e-08 -8.030e-09 -2.741e-08 3.938e-08 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis sigma</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 1.614e-01 -2.900e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent 4.102e-01 -8.030e-09</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M1 -8.109e-01 -2.741e-08</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_M2 5.419e-01 3.938e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis -8.605e-01 -2.681e-08</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_qlogis 1.000e+00 4.971e-08</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 4.971e-08 1.000e+00</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Backtransformed parameters:</span> +<span class="r-out co"><span class="r-pr">#></span> Confidence intervals for internally transformed parameters are asymmetric.</span> +<span class="r-out co"><span class="r-pr">#></span> t-test (unrealistically) based on the assumption of normal distribution</span> +<span class="r-out co"><span class="r-pr">#></span> for estimators of untransformed parameters.</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> FOCUS Chi2 error levels in percent:</span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 8.454 6 17</span> +<span class="r-out co"><span class="r-pr">#></span> parent 8.660 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> M1 10.583 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M2 3.586 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Resulting formation fractions:</span> +<span class="r-out co"><span class="r-pr">#></span> ff</span> +<span class="r-out co"><span class="r-pr">#></span> parent_M1 0.7687</span> +<span class="r-out co"><span class="r-pr">#></span> parent_sink 0.2313</span> +<span class="r-out co"><span class="r-pr">#></span> M1_M2 0.7229</span> +<span class="r-out co"><span class="r-pr">#></span> M1_sink 0.2771</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Estimated disappearance times:</span> +<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.9376 3.114</span> +<span class="r-out co"><span class="r-pr">#></span> M1 2.3170 7.697</span> +<span class="r-out co"><span class="r-pr">#></span> M2 34.2689 113.839</span> +<span class="r-out co"><span class="r-pr">#></span> </span> +<span class="r-out co"><span class="r-pr">#></span> Data:</span> +<span class="r-out co"><span class="r-pr">#></span> time variable observed predicted residual</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.5 1.021e+02 -0.56248</span> +<span class="r-out co"><span class="r-pr">#></span> 0 parent 101.2 1.021e+02 -0.86248</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 53.9 4.873e+01 5.17118</span> +<span class="r-out co"><span class="r-pr">#></span> 1 parent 47.5 4.873e+01 -1.22882</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 10.4 1.111e+01 -0.70773</span> +<span class="r-out co"><span class="r-pr">#></span> 3 parent 7.6 1.111e+01 -3.50773</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 1.1 5.772e-01 0.52283</span> +<span class="r-out co"><span class="r-pr">#></span> 7 parent 0.3 5.772e-01 -0.27717</span> +<span class="r-out co"><span class="r-pr">#></span> 14 parent 3.5 3.264e-03 3.49674</span> +<span class="r-out co"><span class="r-pr">#></span> 28 parent 3.2 1.045e-07 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 parent 0.6 9.530e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 parent 3.5 -5.940e-10 3.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M1 36.4 3.479e+01 1.61088</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M1 37.4 3.479e+01 2.61088</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M1 34.3 3.937e+01 -5.07027</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M1 39.8 3.937e+01 0.42973</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M1 15.1 1.549e+01 -0.38715</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M1 17.8 1.549e+01 2.31285</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M1 5.8 1.995e+00 3.80469</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M1 1.2 1.995e+00 -0.79531</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M1 0.5 2.111e-06 0.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M1 3.2 -9.670e-10 3.20000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 1.5 7.670e-10 1.50000</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M1 0.6 7.670e-10 0.60000</span> +<span class="r-out co"><span class="r-pr">#></span> 1 M2 4.8 4.455e+00 0.34517</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M2 20.9 2.153e+01 -0.62527</span> +<span class="r-out co"><span class="r-pr">#></span> 3 M2 19.3 2.153e+01 -2.22527</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M2 42.0 4.192e+01 0.07941</span> +<span class="r-out co"><span class="r-pr">#></span> 7 M2 43.1 4.192e+01 1.17941</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M2 49.4 4.557e+01 3.83353</span> +<span class="r-out co"><span class="r-pr">#></span> 14 M2 44.3 4.557e+01 -1.26647</span> +<span class="r-out co"><span class="r-pr">#></span> 28 M2 34.6 3.547e+01 -0.87275</span> +<span class="r-out co"><span class="r-pr">#></span> 28 M2 33.0 3.547e+01 -2.47275</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M2 18.8 1.858e+01 0.21837</span> +<span class="r-out co"><span class="r-pr">#></span> 60 M2 17.6 1.858e+01 -0.98163</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M2 10.6 1.013e+01 0.47130</span> +<span class="r-out co"><span class="r-pr">#></span> 90 M2 10.8 1.013e+01 0.67130</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M2 9.8 5.521e+00 4.27893</span> +<span class="r-out co"><span class="r-pr">#></span> 120 M2 3.3 5.521e+00 -2.22107</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -99,44 +42,46 @@ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Three experimental datasets from two water sediment systems and one soil</h1> @@ -149,113 +94,126 @@ software packages (Ranke, 2014).</p> </div> - <pre class="usage"><span class='va'>test_data_from_UBA_2014</span></pre> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> + <p>A list containing three datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>. + Each dataset has, among others, the following components</p><dl><dt><code>title</code></dt> +<dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <dt><code>data</code></dt> +<dd><p>A data frame with the data in the form expected by <code><a href="mkinfit.html">mkinfit</a></code></p></dd> - <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. - Each dataset has, among others, the following components</p><dl> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> -</dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - +</dl></div> + <div id="source"> + <h2>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> - <span class='co'># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span> - <span class='co'># guidance. Due to the strong correlation of the parameter estimates, the</span> - <span class='co'># covariance matrix is not returned. Note that level P-II evaluations are</span> - <span class='co'># generally considered deprecated due to the frequent occurrence of such</span> - <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> - <span class='co'># model).</span> - <span class='va'>m_ws</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent_w <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span><span class='op'>)</span>, - parent_s <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> <span class='va'>f_river</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_ws</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span> -</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_w_0 95.91998118 NA NA NA NA NA -#> k_parent_w 0.41145375 NA NA NA NA NA -#> k_parent_s 0.04663944 NA NA NA NA NA -#> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA -#> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA -#> sigma 3.13612618 NA NA NA NA NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_river</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.1090929 5 6 -#> parent_w 0.0817436 3 3 -#> parent_s 0.1619965 2 3</div><div class='input'> - <span class='co'># This is the evaluation used for the validation of software packages</span> - <span class='co'># in the expertise from 2014</span> - <span class='va'>m_soil</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"M1"</span>, <span class='st'>"M2"</span><span class='op'>)</span><span class='op'>)</span>, - M1 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>, - M2 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"M3"</span><span class='op'>)</span>, - M3 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - <span class='va'>f_soil</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>m_soil</span>, <span class='va'>test_data_from_UBA_2014</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span><span class='op'>$</span><span class='va'>data</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>f_soil</span>, lpos <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span><span class='op'>)</span><span class='op'>)</span> -</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span><span class='op'>$</span><span class='va'>bpar</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower -#> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418 -#> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 -#> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609 -#> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857 -#> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431 -#> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA -#> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA -#> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205 -#> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509 -#> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 -#> Upper -#> parent_0 78.35255358 -#> k_parent 0.13084582 -#> k_M1 6.23970702 -#> k_M2 0.09843260 -#> k_M3 0.04333992 -#> f_parent_to_M1 NA -#> f_parent_to_M2 NA -#> f_M1_to_M3 0.86450775 -#> f_M2_to_M3 0.99489895 -#> sigma 1.45337221</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span><span class='op'>(</span><span class='va'>f_soil</span><span class='op'>)</span> -</div><div class='output co'>#> err.min n.optim df -#> All data 0.09649963 9 20 -#> parent 0.04721283 2 6 -#> M1 0.26551208 2 5 -#> M2 0.20327575 2 5 -#> M3 0.05196550 3 4</div><div class='input'> <span class='co'># }</span> -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span> +<span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span> +<span class="r-in"><span> <span class="co"># covariance matrix is not returned. Note that level P-II evaluations are</span></span></span> +<span class="r-in"><span> <span class="co"># generally considered deprecated due to the frequent occurrence of such</span></span></span> +<span class="r-in"><span> <span class="co"># large parameter correlations, among other reasons (e.g. the adequacy of the</span></span></span> +<span class="r-in"><span> <span class="co"># model).</span></span></span> +<span class="r-in"><span> <span class="va">m_ws</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent_w <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_s"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> parent_s <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"parent_w"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span> <span class="va">f_river</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_ws</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Could not calculate correlation; no covariance matrix</span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w_0 95.91998118 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_w 0.41145375 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_s 0.04663944 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.13612618 NA NA NA NA NA</span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_river</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.1090929 5 6</span> +<span class="r-out co"><span class="r-pr">#></span> parent_w 0.0817436 3 3</span> +<span class="r-out co"><span class="r-pr">#></span> parent_s 0.1619965 2 3</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># This is the evaluation used for the validation of software packages</span></span></span> +<span class="r-in"><span> <span class="co"># in the expertise from 2014</span></span></span> +<span class="r-in"><span> <span class="va">m_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M2 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M3"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> M3 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">f_soil</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">m_soil</span>, <span class="va">test_data_from_UBA_2014</span><span class="op">[[</span><span class="fl">3</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span> +<span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">f_soil</span>, lpos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"topright"</span>, <span class="st">"bottomright"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="test_data_from_UBA_2014-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span><span class="op">$</span><span class="va">bpar</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 76.55425650 0.859186399 89.1008710 1.113861e-26 74.755959418</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 0.84258615 0.806160102 1.0451846 1.545268e-01 0.113779609</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.01122918 0.007245856 1.5497385 6.885052e-02 0.002909431</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 0.32240200 0.240783943 1.3389680 9.819076e-02 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 0.16099855 0.033691952 4.7785464 6.531136e-05 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.27921507 0.269423780 1.0363416 1.565267e-01 0.022978205</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.55641252 0.595119966 0.9349586 1.807707e-01 0.008002509</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778</span> +<span class="r-out co"><span class="r-pr">#></span> Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 78.35255358</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.13084582</span> +<span class="r-out co"><span class="r-pr">#></span> k_M1 6.23970702</span> +<span class="r-out co"><span class="r-pr">#></span> k_M2 0.09843260</span> +<span class="r-out co"><span class="r-pr">#></span> k_M3 0.04333992</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M1 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_M2 NA</span> +<span class="r-out co"><span class="r-pr">#></span> f_M1_to_M3 0.86450775</span> +<span class="r-out co"><span class="r-pr">#></span> f_M2_to_M3 0.99489895</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 1.45337221</span> +<span class="r-in"><span> <span class="fu"><a href="mkinerrmin.html">mkinerrmin</a></span><span class="op">(</span><span class="va">f_soil</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> err.min n.optim df</span> +<span class="r-out co"><span class="r-pr">#></span> All data 0.09649963 9 20</span> +<span class="r-out co"><span class="r-pr">#></span> parent 0.04721283 2 6</span> +<span class="r-out co"><span class="r-pr">#></span> M1 0.26551208 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M2 0.20327575 2 5</span> +<span class="r-out co"><span class="r-pr">#></span> M3 0.05196550 3 4</span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/tex_listing.html b/docs/dev/reference/tex_listing.html index c82138b7..03bd83f2 100644 --- a/docs/dev/reference/tex_listing.html +++ b/docs/dev/reference/tex_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.0</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> @@ -60,7 +60,10 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 75d6a1f9..a7a01043 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -1,72 +1,17 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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transformations are intended to map parameters that should only take on +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms"><meta property="og:description" content="The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the ilr transformation is used." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +the ilr transformation is used."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -77,23 +22,21 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -103,48 +46,50 @@ the ilr transformation is used." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Functions to transform and backtransform kinetic parameters for fitting</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/transform_odeparms.R" class="external-link"><code>R/transform_odeparms.R</code></a></small> <div class="hidden name"><code>transform_odeparms.Rd</code></div> </div> @@ -154,205 +99,221 @@ restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. For compositional parameters, such as the formations fractions that should always sum up to 1 and can not be negative, -the <a href='ilr.html'>ilr</a> transformation is used.</p> +the <a href="ilr.html">ilr</a> transformation is used.</p> + </div> + + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">parms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span> +<span></span> +<span><span class="fu">backtransform_odeparms</span><span class="op">(</span></span> +<span> <span class="va">transparms</span>,</span> +<span> <span class="va">mkinmod</span>,</span> +<span> transform_rates <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> transform_fractions <span class="op">=</span> <span class="cn">TRUE</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> - <pre class="usage"><span class='fu'>transform_odeparms</span><span class='op'>(</span> - <span class='va'>parms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>parms</dt> +<dd><p>Parameters of kinetic models as used in the differential +equations.</p></dd> -<span class='fu'>backtransform_odeparms</span><span class='op'>(</span> - <span class='va'>transparms</span>, - <span class='va'>mkinmod</span>, - transform_rates <span class='op'>=</span> <span class='cn'>TRUE</span>, - transform_fractions <span class='op'>=</span> <span class='cn'>TRUE</span> -<span class='op'>)</span></pre> - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>parms</th> - <td><p>Parameters of kinetic models as used in the differential -equations.</p></td> - </tr> - <tr> - <th>mkinmod</th> - <td><p>The kinetic model of class <a href='mkinmod.html'>mkinmod</a>, containing +<dt>mkinmod</dt> +<dd><p>The kinetic model of class <a href="mkinmod.html">mkinmod</a>, containing the names of the model variables that are needed for grouping the -formation fractions before <a href='ilr.html'>ilr</a> transformation, the parameter -names and the information if the pathway to sink is included in the model.</p></td> - </tr> - <tr> - <th>transform_rates</th> - <td><p>Boolean specifying if kinetic rate constants should +formation fractions before <a href="ilr.html">ilr</a> transformation, the parameter +names and the information if the pathway to sink is included in the model.</p></dd> + + +<dt>transform_rates</dt> +<dd><p>Boolean specifying if kinetic rate constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution of the estimator. If TRUE, also alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS -models and the break point tb of the HS model.</p></td> - </tr> - <tr> - <th>transform_fractions</th> - <td><p>Boolean specifying if formation fractions +models and the break point tb of the HS model.</p></dd> + + +<dt>transform_fractions</dt> +<dd><p>Boolean specifying if formation fractions constants should be transformed in the model specification used in the fitting for better compliance with the assumption of normal distribution of the estimator. The default (TRUE) is to do transformations. The g parameter of the DFOP model is also seen as a fraction. If a single fraction is transformed (g parameter of DFOP or only a single target variable e.g. a single metabolite plus a pathway to sink), a -logistic transformation is used <code><a href='https://rdrr.io/r/stats/Logistic.html'>stats::qlogis()</a></code>. In other cases, i.e. if +logistic transformation is used <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">stats::qlogis()</a></code>. In other cases, i.e. if two or more formation fractions need to be transformed whose sum cannot -exceed one, the <a href='ilr.html'>ilr</a> transformation is used.</p></td> - </tr> - <tr> - <th>transparms</th> - <td><p>Transformed parameters of kinetic models as used in the -fitting procedure.</p></td> - </tr> - </table> +exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd> + - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> +<dt>transparms</dt> +<dd><p>Transformed parameters of kinetic models as used in the +fitting procedure.</p></dd> - <p>A vector of transformed or backtransformed parameters</p> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> +</dl></div> + <div id="value"> + <h2>Value</h2> + +<p>A vector of transformed or backtransformed parameters</p> + </div> + <div id="details"> + <h2>Details</h2> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. -This is no problem for the internal use in <a href='mkinfit.html'>mkinfit</a>.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - +This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</p> + </div> + <div id="author"> + <h2>Author</h2> <p>Johannes Ranke</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> -<span class='va'>SFO_SFO</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='va'>FOCUS_D</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span> <span class='co'># remove zero values to avoid warning</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -<span class='co'># Transformed and backtransformed parameters</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># Compare to the version without transforming rate parameters (does not work</span> -<span class='co'># with analytical solution, we get NA values for m1 in predictions)</span> -<span class='va'>fit.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, transform_rates <span class='op'>=</span> <span class='cn'>FALSE</span>, - solution_type <span class='op'>=</span> <span class='st'>"deSolve"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</div><div class='input'><span class='co'># }</span> - -<span class='va'>initials</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>$</span><span class='va'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>initials</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start</span><span class='op'>)</span> -<span class='va'>transformed</span> <span class='op'><-</span> <span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>$</span><span class='va'>value</span> -<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>transformed</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>$</span><span class='va'>start_transformed</span><span class='op'>)</span> -<span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink -#> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink -#> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -<span class='co'># \dontrun{</span> -<span class='co'># The case of formation fractions (this is now the default)</span> -<span class='va'>SFO_SFO.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> -<span class='va'>fit.ff</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.ff.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.5985 1.5702 96.404 102.79 -#> log_k_parent -2.3157 0.0409 -2.399 -2.23 -#> log_k_m1 -5.2475 0.1332 -5.518 -4.98 -#> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 -#> sigma 3.1255 0.3585 2.396 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 -#> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 -#> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 -#> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 -#> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</div><div class='input'><span class='va'>initials</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"f_parent_to_m1"</span> <span class='op'>=</span> <span class='fl'>0.5</span><span class='op'>)</span> -<span class='va'>transformed</span> <span class='op'><-</span> <span class='fu'>transform_odeparms</span><span class='op'>(</span><span class='va'>initials</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> -<span class='fu'>backtransform_odeparms</span><span class='op'>(</span><span class='va'>transformed</span>, <span class='va'>SFO_SFO.ff</span><span class='op'>)</span> -</div><div class='output co'>#> f_parent_to_m1 -#> 0.5 </div><div class='input'> -<span class='co'># And without sink</span> -<span class='va'>SFO_SFO.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span> - parent <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"m1"</span>, sink <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>, - m1 <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>type <span class='op'>=</span> <span class='st'>"SFO"</span><span class='op'>)</span>, - use_of_ff <span class='op'>=</span> <span class='st'>"max"</span><span class='op'>)</span> -</div><div class='output co'>#> <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'> - -<span class='va'>fit.ff.2</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='va'>SFO_SFO.ff.2</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='va'>fit.ff.2.s</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.ff.2</span><span class='op'>)</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>par</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 84.79 3.012 78.67 90.91 -#> log_k_parent -2.76 0.082 -2.92 -2.59 -#> log_k_m1 -4.21 0.123 -4.46 -3.96 -#> sigma 8.22 0.943 6.31 10.14</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>fit.ff.2.s</span><span class='op'>$</span><span class='va'>bpar</span>, <span class='fl'>3</span><span class='op'>)</span> -</div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower Upper -#> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 -#> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 -#> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 -#> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</div><div class='input'><span class='co'># }</span> - -</div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>, use_of_ff <span class="op">=</span> <span class="st">"min"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Fit the model to the FOCUS example dataset D using defaults</span></span></span> +<span class="r-in"><span><span class="va">FOCUS_D</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># remove zero values to avoid warning</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="co"># Transformed and backtransformed parameters</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.60 1.5702 96.40 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_sink -3.04 0.0763 -3.19 -2.88</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1_sink -5.25 0.1332 -5.52 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.13 0.3585 2.40 3.85</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># Compare to the version without transforming rate parameters (does not work</span></span></span> +<span class="r-in"><span><span class="co"># with analytical solution, we get NA values for m1 in predictions)</span></span></span> +<span class="r-in"><span><span class="va">fit.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, transform_rates <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 96.40384 1.03e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 2.39609 3.85e+00</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">initials</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">$</span><span class="va">value</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">transformed</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">fit</span><span class="op">$</span><span class="va">start_transformed</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 100.750000 -2.302585 -2.301586 -2.300587 </span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent_sink k_parent_m1 k_m1_sink </span> +<span class="r-out co"><span class="r-pr">#></span> 100.7500 0.1000 0.1001 0.1002 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="co"># The case of formation fractions (this is now the default)</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.5985 1.5702 96.404 102.79</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.3157 0.0409 -2.399 -2.23</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -5.2475 0.1332 -5.518 -4.98</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_qlogis 0.0579 0.0893 -0.124 0.24</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.1255 0.3585 2.396 3.85</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069</span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549</span> +<span class="r-in"><span><span class="va">initials</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"f_parent_to_m1"</span> <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">transformed</span> <span class="op"><-</span> <span class="fu">transform_odeparms</span><span class="op">(</span><span class="va">initials</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu">backtransform_odeparms</span><span class="op">(</span><span class="va">transformed</span>, <span class="va">SFO_SFO.ff</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> f_parent_to_m1 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.5 </span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># And without sink</span></span></span> +<span class="r-in"><span><span class="va">SFO_SFO.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> +<span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> use_of_ff <span class="op">=</span> <span class="st">"max"</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO.ff.2</span>, <span class="va">FOCUS_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">fit.ff.2.s</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit.ff.2</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">par</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate Std. Error Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 84.79 3.012 78.67 90.91</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_parent -2.76 0.082 -2.92 -2.59</span> +<span class="r-out co"><span class="r-pr">#></span> log_k_m1 -4.21 0.123 -4.46 -3.96</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.22 0.943 6.31 10.14</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">fit.ff.2.s</span><span class="op">$</span><span class="va">bpar</span>, <span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Estimate se_notrans t value Pr(>t) Lower Upper</span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913</span> +<span class="r-out co"><span class="r-pr">#></span> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075</span> +<span class="r-out co"><span class="r-pr">#></span> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019</span> +<span class="r-out co"><span class="r-pr">#></span> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140</span> +<span class="r-in"><span><span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"> - <h2 data-toc-skip>Contents</h2> - </nav> - </div> + <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> + </nav></div> </div> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/dev/reference/update.mkinfit-1.png b/docs/dev/reference/update.mkinfit-1.png Binary files differindex df8473c1..12fe1f5b 100644 --- a/docs/dev/reference/update.mkinfit-1.png +++ b/docs/dev/reference/update.mkinfit-1.png diff --git a/docs/dev/reference/update.mkinfit-2.png b/docs/dev/reference/update.mkinfit-2.png Binary files differindex 13c99b44..21817f94 100644 --- a/docs/dev/reference/update.mkinfit-2.png +++ b/docs/dev/reference/update.mkinfit-2.png diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html index 83f45028..cf611716 100644 --- a/docs/dev/reference/update.mkinfit.html +++ b/docs/dev/reference/update.mkinfit.html @@ -1,70 +1,15 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> - -<title>Update an mkinfit model with different arguments — update.mkinfit • mkin</title> - - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" /> - -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script> - -<!-- bootstrap-toc --> -<link rel="stylesheet" href="../bootstrap-toc.css"> -<script src="../bootstrap-toc.js"></script> - 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The fitted degradation +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Update an mkinfit model with different arguments — update.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Update an mkinfit model with different arguments — update.mkinfit"><meta property="og:description" content="This function will return an updated mkinfit object. The fitted degradation model parameters from the old fit are used as starting values for the updated fit. Values specified as 'parms.ini' and/or 'state.ini' will -override these starting values." /> - - -<meta name="robots" content="noindex"> - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> - -<!--[if lt IE 9]> +override these starting values."><meta name="robots" content="noindex"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - </head> - - <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> - <header> - <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="container"> <div class="navbar-header"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> @@ -75,23 +20,21 @@ override these starting values." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.2</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> + <ul class="nav navbar-nav"><li> <a href="../reference/index.html">Functions and data</a> </li> <li class="dropdown"> - <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false"> Articles <span class="caret"></span> </a> - <ul class="dropdown-menu" role="menu"> - <li> + <ul class="dropdown-menu" role="menu"><li> <a href="../articles/mkin.html">Introduction to mkin</a> </li> <li> @@ -101,48 +44,50 @@ override these starting values." /> <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> + </li> + <li> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> </li> - </ul> -</li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + </li> + </ul></li> <li> <a href="../news/index.html">News</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/mkin/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/mkin/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </ul></div><!--/.nav-collapse --> </div><!--/.container --> </div><!--/.navbar --> - </header> - -<div class="row"> + </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header"> <h1>Update an mkinfit model with different arguments</h1> - <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/update.mkinfit.R'><code>R/update.mkinfit.R</code></a></small> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/update.mkinfit.R" class="external-link"><code>R/update.mkinfit.R</code></a></small> <div class="hidden name"><code>update.mkinfit.Rd</code></div> </div> @@ -153,66 +98,67 @@ updated fit. Values specified as 'parms.ini' and/or 'state.ini' will override these starting values.</p> </div> - <pre class="usage"><span class='co'># S3 method for mkinfit</span> -<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span>, evaluate <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span></pre> - - <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> - <table class="ref-arguments"> - <colgroup><col class="name" /><col class="desc" /></colgroup> - <tr> - <th>object</th> - <td><p>An mkinfit object to be updated</p></td> - </tr> - <tr> - <th>...</th> - <td><p>Arguments to <code><a href='mkinfit.html'>mkinfit</a></code> that should replace + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, evaluate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>An mkinfit object to be updated</p></dd> + + +<dt>...</dt> +<dd><p>Arguments to <code><a href="mkinfit.html">mkinfit</a></code> that should replace the arguments from the original call. Arguments set to NULL will -remove arguments given in the original call</p></td> - </tr> - <tr> - <th>evaluate</th> - <td><p>Should the call be evaluated or returned as a call</p></td> - </tr> - </table> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='va'>fit</span> <span class='op'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/pkg/saemix/man/subset.html'>subset</a></span><span class='op'>(</span><span class='va'>FOCUS_2006_D</span>, <span class='va'>value</span> <span class='op'>!=</span> <span class='fl'>0</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> -<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent sigma -#> 99.44423885 0.09793574 3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span> -</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='va'>fit_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>fit</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> -<span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> -</div><div class='output co'>#> parent_0 k_parent sigma_low rsd_high -#> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span><span class='op'>(</span><span class='va'>fit_2</span><span class='op'>)</span> -</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> -</div></pre> +remove arguments given in the original call</p></dd> + + +<dt>evaluate</dt> +<dd><p>Should the call be evaluated or returned as a call</p></dd> + +</dl></div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma </span> +<span class="r-out co"><span class="r-pr">#></span> 99.44423885 0.09793574 3.39632469 </span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="update.mkinfit-1.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="va">fit_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fit</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> parent_0 k_parent sigma_low rsd_high </span> +<span class="r-out co"><span class="r-pr">#></span> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </span> +<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_err</a></span><span class="op">(</span><span class="va">fit_2</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="update.mkinfit-2.png" alt="" width="700" height="433"></span> +<span class="r-in"><span><span class="co"># }</span></span></span> +</code></pre></div> + </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - 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