diff options
86 files changed, 1165 insertions, 1102 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 0facf77e..760d8207 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,4 +27,5 @@ Encoding: UTF-8 VignetteBuilder: knitr BugReports: http://github.com/jranke/mkin/issues URL: https://pkgdown.jrwb.de/mkin +Roxygen: list(markdown = TRUE) RoxygenNote: 7.1.0 diff --git a/GNUmakefile b/GNUmakefile index 58d40e52..830b998d 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -100,7 +100,6 @@ articles: vignettes/web_only/FOCUS_Z.html vignettes/web_only/compiled_models.htm pd: roxygen "$(RBIN)/Rscript" -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)" git add -A - git commit -m 'Static documentation rebuilt by pkgdown' -e r-forge: git archive master > $(HOME)/git/mkin/mkin.tar;\ diff --git a/R/mkinfit.R b/R/mkinfit.R index 683a6b3d..c796f06f 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -165,8 +165,12 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' #' Fitting of several models to several datasets in a single call to #' \code{\link{mmkin}}. -#' @source Rocke, David M. und Lorenzato, Stefan (1995) A two-component model -#' for measurement error in analytical chemistry. Technometrics 37(2), 176-184. +#' @references Rocke DM and Lorenzato S (1995) A two-component model +#' for measurement error in analytical chemistry. *Technometrics* 37(2), 176-184. +#' +#' Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +#' Degradation Data. *Environments* 6(12) 124 +#' [doi:10.3390/environments6120124](https://doi.org/10.3390/environments6120124). #' @examples #' #' # Use shorthand notation for parent only degradation @@ -217,7 +221,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables(c("name", "time", "value")) #' } #' #' \dontrun{ -#' # Weighted fits, including IRLS +#' # Weighted fits, including IRLS (error_model = "obs") #' SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), #' m1 = mkinsub("SFO"), use_of_ff = "max") #' f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) diff --git a/R/mkinmod.R b/R/mkinmod.R index 7e9e9248..e58d1e22 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -48,12 +48,17 @@ #' \item{use_of_ff}{ #' The content of \code{use_of_ff} is passed on in this list component. #' } +#' \item{deg_func}{ +#' If generated, a function containing the solution of the degradation +#' model. +#' } #' \item{coefmat}{ #' The coefficient matrix, if the system of differential equations can be #' represented by one. #' } #' \item{cf}{ -#' If generated, the compiled function as returned by cfunction. +#' If generated, a compiled function calculating the derivatives as +#' returned by cfunction. #' } #' @note The IORE submodel is not well tested for metabolites. When using this #' model for metabolites, you may want to read the second note in the help diff --git a/docs/news/index.html b/docs/news/index.html index 3965df70..2874175c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -140,7 +140,7 @@ <div id="mkin-0-9-50-1-unreleased" class="section level1"> <h1 class="page-header" data-toc-text="0.9.50.1"> -<a href="#mkin-0-9-50-1-unreleased" class="anchor"></a>mkin 0.9.50.1 (unreleased)<small> Unreleased </small> +<a href="#mkin-0-9-50-1-unreleased" class="anchor"></a>mkin 0.9.50.1 (unreleased)<small> 2020-05-11 </small> </h1> <ul> <li><p>Support SFORB with formation fractions</p></li> diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index aa796e47..0915d1c8 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: NAFTA_examples: web_only/NAFTA_examples.html benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html -last_built: 2020-05-11T13:20Z +last_built: 2020-05-12T06:36Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 6b782456..b91d40e3 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<link rel="stylesheet" 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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="Calculate the AIC for a column of an mmkin object — AIC.mmkin" /> <meta property="og:description" content="Provides a convenient way to compare different kinetic models fitted to the same dataset." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ same dataset." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -70,7 +73,7 @@ same dataset." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -114,7 +117,12 @@ same dataset." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -129,7 +137,7 @@ same dataset." /> <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='http://github.com/jranke/mkin/blob/master/R/AIC.mmkin.R'><code>R/AIC.mmkin.R</code></a></small> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -165,7 +173,7 @@ column.</p></td> <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> +dataframe if there are several fits in the column).</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -181,13 +189,13 @@ column.</p></td> <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='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC #> SFO 3 55.28197 -#> FOMC 4 57.28202 +#> FOMC 4 57.28211 #> 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='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</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 49.28202 +#> FOMC 4 49.28211 #> 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='no'>f</span>[, <span class='st'>"FOCUS A"</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 57.59979 +#> FOMC 4 57.59987 #> 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='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC @@ -200,16 +208,10 @@ column.</p></td> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -220,7 +222,7 @@ column.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 84e33f9e..e0094738 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -73,7 +73,7 @@ two exponential decline functions." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -180,15 +180,15 @@ kinetic constant.</p></td> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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>Other parent solutions: diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 369398d5..f8fbd2ba 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -73,7 +73,7 @@ a decreasing rate constant." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -181,23 +181,23 @@ in the original equation.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The solution of the FOMC kinetic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and - <code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> +<code><a href='SFO.solution.html'>SFO.solution</a></code> for large values of <code>alpha</code> and +<code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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> <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, - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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> <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: - A new model based on spatial variability. <em>Environmental Science and - Technology</em> <b>24</b>, 1032-1038</p> +A new model based on spatial variability. <em>Environmental Science and +Technology</em> <b>24</b>, 1032-1038</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Other parent solutions: diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 2684ee60..9404893c 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -73,7 +73,7 @@ between them." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -181,15 +181,15 @@ according to <code>k2</code>.</p></td> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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>Other parent solutions: diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index f197cb08..194d11aa 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -73,7 +73,7 @@ a concentration dependent rate constant." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -176,13 +176,13 @@ units used.</p></td> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The solution of the IORE kinetic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. The parameters of the IORE model can - be transformed to equivalent parameters of the FOMC mode - see the NAFTA - guidance for details.</p> +<code><a href='SFO.solution.html'>SFO.solution</a></code> if N = 1. The parameters of the IORE model can +be transformed to equivalent parameters of the FOMC mode - see the NAFTA +guidance for details.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance - for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> +for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Other parent solutions: diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 9664deb3..b263f2f3 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -72,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -169,15 +169,15 @@ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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>Other parent solutions: diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 504f209f..4ef85274 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -76,7 +76,7 @@ and no substance in the bound fraction." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -183,19 +183,19 @@ fraction.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>The value of the response variable, which is the sum of free and - bound fractions at time <code>t</code>.</p> +bound fractions at time <code>t</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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>Other parent solutions: diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 3018ff7f..88806d7b 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex d476bba1..6a806c2d 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 298f2ebd..1919a566 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index ab499a19..c25bbe17 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<link rel="stylesheet" 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-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -39,7 +43,6 @@ <meta property="og:description" content="Normally distributed errors are added to data predicted for a specific degradation model using mkinpredict. The variance of the error may depend on the predicted value and is specified as a standard deviation." /> -<meta name="twitter:card" content="summary" /> @@ -57,7 +60,7 @@ may depend on the predicted value and is specified as a standard deviation." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -71,7 +74,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -115,7 +118,12 @@ may depend on the predicted value and is specified as a standard deviation." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -130,7 +138,7 @@ may depend on the predicted value and is specified as a standard deviation." /> <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='http://github.com/jranke/mkin/blob/master/R/add_err.R'><code>R/add_err.R</code></a></small> <div class="hidden name"><code>add_err.Rd</code></div> </div> @@ -197,7 +205,7 @@ seed is not set.</p></td> <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> +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> <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is @@ -236,28 +244,21 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> <span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</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.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</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.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -268,7 +269,7 @@ http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 1dd6288b..7658a572 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -44,7 +48,6 @@ 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="twitter:card" content="summary" /> @@ -62,7 +65,7 @@ method of Venzon and Moolgavkar (1988)." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -76,7 +79,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -120,7 +123,12 @@ method of Venzon and Moolgavkar (1988)." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -135,7 +143,7 @@ method of Venzon and Moolgavkar (1988)." /> <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='http://github.com/jranke/mkin/blob/master/R/confint.mkinfit.R'><code>R/confint.mkinfit.R</code></a></small> <div class="hidden name"><code>confint.mkinfit.Rd</code></div> </div> @@ -212,7 +220,7 @@ their confidence intervals?</p></td> </tr> <tr> <th>cores</th> - <td><p>The number of cores to be used for multicore processing. + <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> @@ -228,15 +236,15 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <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> +each parameter.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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> +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> +Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, +87–94.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) @@ -262,50 +270,71 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='error'>Error in mkinpredict.mkinmod(mkinmod, parms, odeini, outtimes, solution_type = solution_type, use_compiled = use_compiled, method.ode = method.ode, atol = atol, rtol = rtol, ...): Differential equations were not integrated for all output times because</span> -#> <span class='error'>NaN values occurred in output from ode()</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 11.39 0 11.4</span></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='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> User System verstrichen +#> 3.362 0.000 3.364 </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 from about 50</span> <span class='co'># seconds to about 12 seconds if we use at least four cores</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile_no_parent_0</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, - <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> User System verstrichen -#> 20.058 0.122 11.784 </div><div class='input'><span class='no'>ci_profile</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) -<span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841641 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='no'>ci_quadratic_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) -<span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403841648 102.79312450 -#> 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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></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='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>))</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> <span class='warning'>Warning: scheduled cores 1, 2, 3 encountered errors in user code, all values of the jobs will be affected</span></div><div class='output co'>#> <span class='error'>Error in dimnames(x) <- dn: Länge von 'dimnames' [2] ungleich der Arrayausdehnung</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.011 0.045 0.201</span></div><div class='input'><span class='no'>ci_profile</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 0.003892605 6.702778e-03 +#> f_parent_to_m1 0.471328495 5.611550e-01 +#> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) +<span class='no'>ci_quadratic_transformed</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403839460 1.027931e+02 +#> k_parent 0.090823790 1.072543e-01 +#> k_m1 0.004012216 6.897547e-03 +#> f_parent_to_m1 0.469118713 5.595960e-01 +#> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) +<span class='no'>ci_quadratic_untransformed</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 96.403839413 1.027931e+02 +#> k_parent 0.090491931 1.069035e-01 +#> k_m1 0.003835483 6.685819e-03 +#> f_parent_to_m1 0.469113365 5.598386e-01 +#> sigma 2.396089689 3.854918e+00</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='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'ci_profile' nicht gefunden</span></div><div class='input'><span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_transformed' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/Round.html'>signif</a></span>(<span class='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'rel_diffs_untransformed' nicht gefunden</span></div><div class='input'> +<span class='no'>rel_diffs_transformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) +<span class='no'>rel_diffs_untransformed</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed</span> - <span class='no'>ci_profile</span>)/<span class='no'>ci_profile</span>) +<span class='no'>rel_diffs_transformed</span> <span class='kw'><</span> <span class='no'>rel_diffs_untransformed</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 TRUE TRUE +#> k_parent TRUE TRUE +#> k_m1 FALSE FALSE +#> f_parent_to_m1 TRUE 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='no'>rel_diffs_transformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent 0.000960 0.000900 +#> k_m1 0.030700 0.029100 +#> f_parent_to_m1 0.004690 0.002780 +#> 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='no'>rel_diffs_untransformed</span>, <span class='fl'>3</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 0.000541 0.000222 +#> k_parent 0.004610 0.002370 +#> k_m1 0.014700 0.002530 +#> f_parent_to_m1 0.004700 0.002350 +#> sigma 0.055000 0.032700</div><div class='input'> <span class='co'># Investigate a case with formation fractions</span> <span class='no'>f_d_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>ci_profile_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='no'>n_cores</span>)</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='input'><span class='no'>ci_profile_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.456003650 1.027703e+02 +#> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 #> k_m1 0.003892605 6.702778e-03 #> f_parent_to_m1 0.471328495 5.611550e-01 #> sigma 2.535612399 3.985263e+00</div><div class='input'><span class='no'>ci_quadratic_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>) <span class='no'>ci_quadratic_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839992 1.027931e+02 +#> parent_0 96.403839460 1.027931e+02 #> k_parent 0.090823790 1.072543e-01 #> k_m1 0.004012216 6.897547e-03 -#> f_parent_to_m1 0.469118711 5.595960e-01 +#> f_parent_to_m1 0.469118713 5.595960e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>ci_quadratic_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) <span class='no'>ci_quadratic_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 96.403839944 1.027931e+02 +#> parent_0 96.403839413 1.027931e+02 #> k_parent 0.090491931 1.069035e-01 #> k_m1 0.003835483 6.685819e-03 -#> f_parent_to_m1 0.469113362 5.598386e-01 +#> f_parent_to_m1 0.469113365 5.598386e-01 #> sigma 2.396089689 3.854918e+00</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_transformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='no'>rel_diffs_untransformed_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/MathFun.html'>abs</a></span>((<span class='no'>ci_quadratic_untransformed_ff</span> - <span class='no'>ci_profile_ff</span>)/<span class='no'>ci_profile_ff</span>) <span class='co'># While the confidence interval for the parent rate constant is closer to</span> @@ -318,15 +347,15 @@ On Windows machines, cores > 1 is currently not supported.</p></td> #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE #> sigma FALSE FALSE</div><div class='input'><span class='no'>rel_diffs_transformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408026 0.0002217846 -#> k_parent 0.0009596414 0.0009003877 -#> k_m1 0.0307277403 0.0290579212 -#> f_parent_to_m1 0.0046884168 0.0027782604 +#> parent_0 0.0005408080 0.0002217794 +#> k_parent 0.0009596417 0.0009003876 +#> k_m1 0.0307277370 0.0290579182 +#> f_parent_to_m1 0.0046884130 0.0027782556 #> sigma 0.0550252516 0.0327066836</div><div class='input'><span class='no'>rel_diffs_untransformed_ff</span></div><div class='output co'>#> 2.5% 97.5% -#> parent_0 0.0005408031 0.0002217851 -#> k_parent 0.0046100089 0.0023730230 -#> k_m1 0.0146746442 0.0025300972 -#> f_parent_to_m1 0.0046997642 0.0023460268 +#> parent_0 0.0005408085 0.0002217799 +#> k_parent 0.0046100096 0.0023730229 +#> k_m1 0.0146746469 0.0025301011 +#> f_parent_to_m1 0.0046997599 0.0023460223 #> 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> @@ -337,29 +366,24 @@ On Windows machines, cores > 1 is currently not supported.</p></td> <span class='no'>DFOP_par_c</span> <span class='kw'><-</span> <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span> <span class='no'>f_tc_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>DFOP_par_c</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='st'>"direct"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.596218141 106.19934683 -#> k_M1 0.037605440 0.04490756 -#> k_M2 0.008568747 0.01087674 -#> f_parent_to_M1 0.021466788 0.62023878 -#> f_parent_to_M2 0.015168650 0.37975352 -#> k1 0.273897581 0.33388066 -#> k2 0.018614556 0.02250379 -#> g 0.671943831 0.73583255 -#> sigma_low 0.251283700 0.83992071 -#> rsd_high 0.040411017 0.07662005</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% -#> parent_0 94.59622 106.1993</div><div class='input'># } +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.59613833 106.19939215 +#> k_M1 0.03760542 0.04490759 +#> k_M2 0.00856874 0.01087675 +#> f_parent_to_M1 0.02146166 0.62023888 +#> f_parent_to_M2 0.01516502 0.37975343 +#> k1 0.27389751 0.33388078 +#> k2 0.01861456 0.02250379 +#> g 0.67194349 0.73583256 +#> sigma_low 0.25128383 0.83992146 +#> rsd_high 0.04041100 0.07662001</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_tc_2</span>, <span class='st'>"parent_0"</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 94.59614 106.1994</div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -370,7 +394,7 @@ On Windows machines, cores > 1 is currently not supported.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index ef38c521..05d65191 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -11,23 +11,27 @@ with mkinfit — endpoints • mkin</title> <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -43,7 +47,6 @@ from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites." /> -<meta name="twitter:card" content="summary" /> @@ -61,7 +64,7 @@ advantage that the SFORB model can also be used for metabolites." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -75,7 +78,7 @@ advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -119,7 +122,12 @@ advantage that the SFORB model can also be used for metabolites." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -135,7 +143,7 @@ advantage that the SFORB model can also be used for metabolites." /> <div class="page-header"> <h1>Function to calculate endpoints for further use from kinetic models fitted with mkinfit</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/endpoints.R'><code>R/endpoints.R</code></a></small> <div class="hidden name"><code>endpoints.Rd</code></div> </div> @@ -162,9 +170,9 @@ advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with a matrix of dissipation times named distimes, - and, if applicable, a vector of formation fractions named ff - and, if the SFORB model was in use, a vector of eigenvalues - of these SFORB models, equivalent to DFOP rate constants</p> +and, if applicable, a vector of formation fractions named ff +and, if the SFORB model was in use, a vector of eigenvalues +of these SFORB models, equivalent to DFOP rate constants</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The function is used internally by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> @@ -192,17 +200,10 @@ advantage that the SFORB model can also be used for metabolites.</p> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#note">Note</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -213,7 +214,7 @@ advantage that the SFORB model can also be used for metabolites.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html index c5b8e38c..598a25c0 100644 --- a/docs/reference/get_deg_func.html +++ b/docs/reference/get_deg_func.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -37,7 +41,6 @@ <meta property="og:title" content="Retrieve a degradation function from the mmkin namespace — get_deg_func" /> <meta property="og:description" content="Retrieve a degradation function from the mmkin namespace" /> -<meta name="twitter:card" content="summary" /> @@ -55,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -69,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -113,7 +116,12 @@ </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -128,7 +136,7 @@ <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='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> <div class="hidden name"><code>get_deg_func.Rd</code></div> </div> @@ -142,15 +150,13 @@ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A function that was likely previously assigned from within - nlme.mmkin</p> +nlme.mmkin</p> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#value">Value</a></li> - </ul> - + <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> @@ -161,7 +167,7 @@ </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 76ce2233..8410e499 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> <meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ transformations." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -70,7 +73,7 @@ transformations." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -114,7 +117,12 @@ transformations." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -129,7 +137,7 @@ transformations." /> <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='http://github.com/jranke/mkin/blob/master/R/ilr.R'><code>R/ilr.R</code></a></small> <div class="hidden name"><code>ilr.Rd</code></div> </div> @@ -155,16 +163,16 @@ sensible for vectors with all elements being greater than zero.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <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> +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> <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for - Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> +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 - <code>robCompositions</code>.</p></div> +<code>robCompositions</code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -180,18 +188,10 @@ sensible for vectors with all elements being greater than zero.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span>(<span class='no'>b</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='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://rdrr.io/r/base/sum.html'>sum</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</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> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>René Lehmann and Johannes Ranke</p> + <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> @@ -202,7 +202,7 @@ sensible for vectors with all elements being greater than zero.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 9a54496e..8e33c28f 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<link rel="stylesheet" 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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -41,7 +45,6 @@ observed value, as calculated as part of the fitting procedure using dnorm, i.e. assuming normal distribution, and with the means predicted by the degradation model, and the standard deviations predicted by the error model." /> -<meta name="twitter:card" content="summary" /> @@ -59,7 +62,7 @@ the error model." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ the error model." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ the error model." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ the error model." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Calculated the log-likelihood of a fitted mkinfit object</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logLik.mkinfit.R'><code>R/logLik.mkinfit.R</code></a></small> <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> </div> @@ -163,8 +171,8 @@ the error model.</p> <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 - parameters (degradation model parameters plus variance model parameters) - as attribute.</p> +parameters (degradation model parameters plus variance model parameters) +as attribute.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The total number of estimated parameters returned with the value of the @@ -173,7 +181,7 @@ 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> +<code><a href='AIC.mmkin.html'>AIC.mmkin</a></code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -189,18 +197,10 @@ and the fitted error model parameters.</p> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -211,7 +211,7 @@ and the fitted error model parameters.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index b0ec77b1..9907297c 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -73,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -179,19 +179,19 @@ an increasing rate constant, supposedly caused by microbial growth</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The solution of the logistic model reduces to the - <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p> +<code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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>Other parent solutions: diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index ef2a55bf..b8ce5397 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -11,23 +11,27 @@ kinetic models fitted with mkinfit — max_twa_parent • mkin</title> <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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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href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -43,7 +47,6 @@ concentrations (TWAs) for kinetic models fitted with mkinfit. 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="twitter:card" content="summary" /> @@ -61,7 +64,7 @@ soil section of the FOCUS guidance." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -75,7 +78,7 @@ soil section of the FOCUS guidance." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -119,7 +122,12 @@ soil section of the FOCUS guidance." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -135,7 +143,7 @@ soil section of the FOCUS guidance." /> <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='http://github.com/jranke/mkin/blob/master/R/max_twa_parent.R'><code>R/max_twa_parent.R</code></a></small> <div class="hidden name"><code>max_twa_parent.Rd</code></div> </div> @@ -213,15 +221,15 @@ factor (f_twa) is calculated.</p></td> <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 - <code>windows</code> argument. For the other functions, a numeric vector of - length one (also known as 'a number').</p> +<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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -230,17 +238,10 @@ factor (f_twa) is calculated.</p></td> #> 34.71343 18.22124 </div><div class='input'> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -251,7 +252,7 @@ factor (f_twa) is calculated.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 46a80308..c5d3495f 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 47f48b72..7e5a00f2 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -41,7 +45,6 @@ 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 plot.mkinfit using the argument show_errplot = TRUE." /> -<meta name="twitter:card" content="summary" /> @@ -59,7 +62,7 @@ using the argument show_errplot = TRUE." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ using the argument show_errplot = TRUE." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ using the argument show_errplot = TRUE." /> <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='http://github.com/jranke/mkin/blob/master/R/mkinerrplot.R'><code>R/mkinerrplot.R</code></a></small> <div class="hidden name"><code>mkinerrplot.Rd</code></div> </div> @@ -212,18 +220,18 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </tr> <tr> <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td> + <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.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> +effect, namely to produce a plot.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>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> +lines of the mkinfit object.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -232,17 +240,10 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -253,7 +254,7 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 9974b66b..ceac59bf 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -78,7 +78,7 @@ likelihood function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -209,15 +209,15 @@ detection.</p></td> <tr> <th>parms.ini</th> <td><p>A named vector of initial values for the parameters, - including parameters to be optimised and potentially also fixed parameters - as indicated by <code>fixed_parms</code>. If set to "auto", initial values for - rate constants are set to default values. Using parameter names that are - not in the model gives an error.</p> +including parameters to be optimised and potentially also fixed parameters +as indicated by <code>fixed_parms</code>. If set to "auto", initial values for +rate constants are set to default values. Using parameter names that are +not in the model gives an error.</p> <p>It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from - this model. This works nicely if the models are nested. An example is - given below.</p></td> +needs. You can use the parameter lists "bparms.ode" from a previously +fitted model, which contains the differential equation parameters from +this model. This works nicely if the models are nested. An example is +given below.</p></td> </tr> <tr> <th>state.ini</th> @@ -326,42 +326,44 @@ is 1e-10, much lower than in <code>lsoda</code>.</p></td> <tr> <th>error_model</th> <td><p>If the error model is "const", a constant standard - deviation is assumed.</p> +deviation is assumed.</p> <p>If the error model is "obs", each observed variable is assumed to have its - own variance.</p> +own variance.</p> <p>If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model - deviates from the model by Rocke and Lorenzato, as their model implies - that the errors follow a lognormal distribution for large values, not a - normal distribution as assumed by this method.</p></td> +error model similar to the one described by Rocke and Lorenzato (1995) is +used for setting up the likelihood function. Note that this model +deviates from the model by Rocke and Lorenzato, as their model implies +that the errors follow a lognormal distribution for large values, not a +normal distribution as assumed by this method.</p></td> </tr> <tr> <th>error_model_algorithm</th> <td><p>If "auto", the selected algorithm depends on - the error model. If the error model is "const", unweighted nonlinear - least squares fitting ("OLS") is selected. If the error model is "obs", or - "tc", the "d_3" algorithm is selected.</p> -<p>The algorithm "d_3" will directly minimize the negative log-likelihood and - - independently - also use the three step algorithm described below. The - fit with the higher likelihood is returned.</p> +the error model. If the error model is "const", unweighted nonlinear +least squares fitting ("OLS") is selected. If the error model is "obs", or +"tc", the "d_3" algorithm is selected.</p> +<p>The algorithm "d_3" will directly minimize the negative log-likelihood and</p><ul> +<li><p>independently - also use the three step algorithm described below. The +fit with the higher likelihood is returned.</p></li> +</ul> + <p>The algorithm "direct" will directly minimize the negative log-likelihood.</p> <p>The algorithm "twostep" will minimize the negative log-likelihood after an - initial unweighted least squares optimisation step.</p> +initial unweighted least squares optimisation step.</p> <p>The algorithm "threestep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, and then minimizes the negative log-likelihood with free - degradation and error model parameters.</p> +optimizes only the error model using the degradation model parameters +found, and then minimizes the negative log-likelihood with free +degradation and error model parameters.</p> <p>The algorithm "fourstep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, then optimizes the degradation model again with fixed error model - parameters, and finally minimizes the negative log-likelihood with free - degradation and error model parameters.</p> +optimizes only the error model using the degradation model parameters +found, then optimizes the degradation model again with fixed error model +parameters, and finally minimizes the negative log-likelihood with free +degradation and error model parameters.</p> <p>The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error - model parameters and subsequent optimization of the degradation model - using those error model parameters, until the error model parameters - converge.</p></td> +unweighted least squares, and then iterates optimization of the error +model parameters and subsequent optimization of the degradation model +using those error model parameters, until the error model parameters +converge.</p></td> </tr> <tr> <th>reweight.tol</th> @@ -383,14 +385,10 @@ the error model parameters in IRLS fits.</p></td> </tr> </table> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model - for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list with "mkinfit" in the class attribute. A summary can be - obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> +obtained by <code><a href='summary.mkinfit.html'>summary.mkinfit</a></code>.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>Per default, parameters in the kinetic models are internally transformed in @@ -399,33 +397,40 @@ estimators.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>When using the "IORE" submodel for metabolites, fitting with - "transform_rates = TRUE" (the default) often leads to failures of the - numerical ODE solver. In this situation it may help to switch off the - internal rate transformation.</p> +"transform_rates = TRUE" (the default) often leads to failures of the +numerical ODE solver. In this situation it may help to switch off the +internal rate transformation.</p> + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Rocke DM and Lorenzato S (1995) A two-component model +for measurement error in analytical chemistry. <em>Technometrics</em> 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 +<a href='https://doi.org/10.3390/environments6120124'>doi:10.3390/environments6120124</a>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Plotting methods <code><a href='plot.mkinfit.html'>plot.mkinfit</a></code> and - <code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> +<code><a href='mkinparplot.html'>mkinparplot</a></code>.</p> <p>Comparisons of models fitted to the same data can be made using - <code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code> by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> +<code><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></code> by virtue of the method <code><a href='logLik.mkinfit.html'>logLik.mkinfit</a></code>.</p> <p>Fitting of several models to several datasets in a single call to - <code><a href='mmkin.html'>mmkin</a></code>.</p></div> +<code><a href='mmkin.html'>mmkin</a></code>.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># Use shorthand notation for parent only degradation</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.1 #> R version used for fitting: 4.0.0 -#> Date of fit: Mon May 11 05:14:26 2020 -#> Date of summary: Mon May 11 05:14:26 2020 +#> Date of fit: Tue May 12 08:36:07 2020 +#> Date of summary: Tue May 12 08:36:07 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.043 s +#> Fitted using 222 model solutions performed in 0.047 s #> #> Error model: Constant variance #> @@ -502,7 +507,7 @@ estimators.</p> <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>#> User System verstrichen -#> 0.407 0.002 0.409 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.408 0.008 0.416 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598483222 0.098697734 0.005260651 0.514475962 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -592,7 +597,7 @@ estimators.</p> #> Sum of squared residuals at call 166: 371.2134 #> Sum of squared residuals at call 168: 371.2134 #> Negative log-likelihood at call 178: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 0.349 0.000 0.350 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma +#> 0.350 0.001 0.351 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma #> 99.598480759 0.098697739 0.005260651 0.514475958 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_m1 parent_sink #> 0.514476 0.485524 @@ -622,12 +627,12 @@ estimators.</p> <span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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: Initial parameter(s) k_parent_free_sink not used in the model</span></div><div class='input'><span class='co'># }</span> <span class='co'># \dontrun{</span> -<span class='co'># Weighted fits, including IRLS</span> +<span class='co'># Weighted fits, including IRLS (error_model = "obs")</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.1 #> R version used for fitting: 4.0.0 -#> Date of fit: Mon May 11 05:14:31 2020 -#> Date of summary: Mon May 11 05:14:31 2020 +#> Date of fit: Tue May 12 08:36:12 2020 +#> Date of summary: Tue May 12 08:36:12 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -635,7 +640,7 @@ estimators.</p> #> #> Model predictions using solution type analytical #> -#> Fitted using 421 model solutions performed in 0.124 s +#> Fitted using 421 model solutions performed in 0.146 s #> #> Error model: Constant variance #> @@ -746,10 +751,10 @@ estimators.</p> #> 100 m1 31.04 31.98163 -9.416e-01 #> 100 m1 33.13 31.98163 1.148e+00 #> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.1 #> R version used for fitting: 4.0.0 -#> Date of fit: Mon May 11 05:14:32 2020 -#> Date of summary: Mon May 11 05:14:32 2020 +#> Date of fit: Tue May 12 08:36:13 2020 +#> Date of summary: Tue May 12 08:36:13 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -757,7 +762,7 @@ estimators.</p> #> #> Model predictions using solution type analytical #> -#> Fitted using 978 model solutions performed in 0.336 s +#> Fitted using 978 model solutions performed in 0.337 s #> #> Error model: Variance unique to each observed variable #> @@ -883,10 +888,10 @@ estimators.</p> #> 100 m1 31.04 31.98773 -9.477e-01 #> 100 m1 33.13 31.98773 1.142e+00 #> 120 m1 25.15 28.80429 -3.654e+00 -#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50 +#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.50.1 #> R version used for fitting: 4.0.0 -#> Date of fit: Mon May 11 05:14:32 2020 -#> Date of summary: Mon May 11 05:14:32 2020 +#> Date of fit: Tue May 12 08:36:14 2020 +#> Date of summary: Tue May 12 08:36:14 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -894,7 +899,7 @@ estimators.</p> #> #> Model predictions using solution type analytical #> -#> Fitted using 1875 model solutions performed in 0.642 s +#> Fitted using 1875 model solutions performed in 0.647 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 81b62ae1..1c97048e 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -75,7 +75,7 @@ list of lists can be given in the speclist argument." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -205,15 +205,18 @@ applicable to give detailed information about the C function being built.</p></t <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, - containing, among others,</p> +containing, among others,</p> <dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for - each modelling variable.</p></dd> - <dt>map</dt><dd><p>A list containing named character vectors for each observed variable, - specifying the modelling variables by which it is represented.</p></dd> - <dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> - <dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be - represented by one.</p></dd> - <dt>cf</dt><dd><p>If generated, the compiled function as returned by cfunction.</p></dd> +each modelling variable.</p></dd> +<dt>map</dt><dd><p>A list containing named character vectors for each observed variable, +specifying the modelling variables by which it is represented.</p></dd> +<dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd> +<dt>deg_func</dt><dd><p>If generated, a function containing the solution of the degradation +model.</p></dd> +<dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be +represented by one.</p></dd> +<dt>cf</dt><dd><p>If generated, a compiled function calculating the derivatives as +returned by cfunction.</p></dd> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> @@ -222,17 +225,17 @@ in the FOCUS and NAFTA guidance documents are used.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>The IORE submodel is not well tested for metabolites. When using this - model for metabolites, you may want to read the second note in the help - page to <code><a href='mkinfit.html'>mkinfit</a></code>.</p> +model for metabolites, you may want to read the second note in the help +page to <code><a href='mkinfit.html'>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 - and Degradation Kinetics from Environmental Fate Studies on Pesticides in - 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental Media</p> +Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -252,7 +255,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file1a1abf38df.c 2> file1a1abf38df.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file15d32c282a7d.c 2> file15d32c282a7d.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot-1.png b/docs/reference/mkinparplot-1.png Binary files differindex d4259579..6853a4ba 100644 --- a/docs/reference/mkinparplot-1.png +++ b/docs/reference/mkinparplot-1.png diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index af936795..dfe695d0 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> <meta property="og:description" content="This function plots the confidence intervals for the parameters fitted using mkinfit." /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ mkinfit." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -70,7 +73,7 @@ mkinfit." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -114,7 +117,12 @@ mkinfit." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -129,7 +137,7 @@ mkinfit." /> <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='http://github.com/jranke/mkin/blob/master/R/mkinparplot.R'><code>R/mkinparplot.R</code></a></small> <div class="hidden name"><code>mkinparplot.Rd</code></div> </div> @@ -152,7 +160,7 @@ mkinfit." /> <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> +effect, namely to produce a plot.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -163,16 +171,10 @@ mkinfit." /> <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -183,7 +185,7 @@ mkinfit." /> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex d29181c3..bb9657b4 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 698af302..cd6bf4a1 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -40,7 +44,6 @@ 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="twitter:card" content="summary" /> @@ -58,7 +61,7 @@ argument show_residuals = TRUE." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -72,7 +75,7 @@ argument show_residuals = TRUE." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -116,7 +119,12 @@ argument show_residuals = TRUE." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -131,7 +139,7 @@ argument show_residuals = TRUE." /> <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='http://github.com/jranke/mkin/blob/master/R/mkinresplot.R'><code>R/mkinresplot.R</code></a></small> <div class="hidden name"><code>mkinresplot.Rd</code></div> </div> @@ -216,36 +224,29 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </tr> <tr> <th>...</th> - <td><p>further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></code>.</p></td> + <td><p>further arguments passed to <code><a href='https://rdrr.io/r/base/plot.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> +effect, namely to produce a plot.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>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> +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="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -256,7 +257,7 @@ be passed on to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 328cec9b..135d5446 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 7b1d73d5..40109afc 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 4c412abc..bce34531 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 201ef0fd..02976ced 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png diff --git a/docs/reference/mmkin-5.png b/docs/reference/mmkin-5.png Binary files differindex 29206932..56750342 100644 --- a/docs/reference/mmkin-5.png +++ b/docs/reference/mmkin-5.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index c1f62be7..db359f48 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -11,23 +11,27 @@ more datasets — mmkin • mkin</title> <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -40,7 +44,6 @@ more datasets — mmkin • mkin</title> more datasets — mmkin" /> <meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets specified in its first two arguments." /> -<meta name="twitter:card" content="summary" /> @@ -58,7 +61,7 @@ datasets specified in its first two arguments." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -72,7 +75,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -116,7 +119,12 @@ datasets specified in its first two arguments." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ datasets specified in its first two arguments." /> <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='http://github.com/jranke/mkin/blob/master/R/mmkin.R'><code>R/mmkin.R</code></a></small> <div class="hidden name"><code>mmkin.Rd</code></div> </div> @@ -184,12 +192,12 @@ for parallel execution.</p></td> <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 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> +objects 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> <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> +plotting.</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -205,42 +213,35 @@ for parallel execution.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) <span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) -<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) - +<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 16.471 0.352 5.654 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.578 0.000 19.590 </div><div class='input'> +#> 4.370 0.401 1.265 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 5.000 0.008 5.011 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink -#> 0.7340480 0.2659520 0.7505686 0.2494314 +#> 0.7340478 0.2659522 0.7505691 0.2494309 #> #> $distimes #> DT50 DT90 -#> parent 0.8777689 2.915885 -#> M1 2.3257452 7.725958 -#> M2 33.7200890 112.015711 +#> parent 0.8777688 2.915885 +#> M1 2.3257466 7.725963 +#> M2 33.7200800 112.015681 #> </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.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</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.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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.html'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</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='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</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/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</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.html'>plot</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]]) +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># } +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -251,7 +252,7 @@ for parallel execution.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 60917ff4..02c44737 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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" 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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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -41,7 +45,6 @@ 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="twitter:card" content="summary" /> @@ -59,7 +62,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP." /> <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='http://github.com/jranke/mkin/blob/master/R/nafta.R'><code>R/nafta.R</code></a></small> <div class="hidden name"><code>nafta.Rd</code></div> </div> @@ -186,20 +194,20 @@ dissipation times.</p></td> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>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> - accessed 2019-02-22</p> +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> +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> +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> <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> +<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="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> @@ -240,20 +248,13 @@ dissipation times.</p></td> #> 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.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> +#> [1] 841.41</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -264,7 +265,7 @@ dissipation times.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index b92d2141..78489ee7 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -75,7 +75,7 @@ datasets." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -173,9 +173,9 @@ datasets.</p> <p>A function that can be used with nlme</p> <p>If random is FALSE (default), a named vector containing mean values - of the fitted degradation model parameters. If random is TRUE, a list with - fixed and random effects, in the format required by the start argument of - nlme for the case of a single grouping variable ds?</p> +of the fitted degradation model parameters. If random is TRUE, a list with +fixed and random effects, in the format required by the start argument of +nlme for the case of a single grouping variable ds?</p> <p>A <code><a href='https://rdrr.io/pkg/nlme/man/groupedData.html'>groupedData</a></code> object</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 67bd07de..67f279da 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex ee6bb2e4..16a5d7bd 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex 1d5569e9..73426834 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git 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-10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -39,7 +43,6 @@ <meta property="og:description" content="This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets." /> -<meta name="twitter:card" content="summary" /> @@ -57,7 +60,7 @@ have been obtained by fitting the same model to a list of datasets." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -71,7 +74,7 @@ have been obtained by fitting the same model to a list of datasets." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -115,7 +118,12 @@ have been obtained by fitting the same model to a list of datasets." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -130,7 +138,7 @@ have been obtained by fitting the same model to a list of datasets." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Create an nlme model for an mmkin row object</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.mmkin.R'><code>R/nlme.mmkin.R</code></a></small> <div class="hidden name"><code>nlme.mmkin.Rd</code></div> </div> @@ -243,7 +251,7 @@ parameters taken from the mmkin object are used</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>Upon success, a fitted nlme.mmkin object, which is an nlme object - with additional elements</p> +with additional elements</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='nlme.html'>nlme_function</a></code></p></div> @@ -309,142 +317,124 @@ parameters taken from the mmkin object are used</p></td> <span class='st'>"FOMC-SFO"</span> <span class='kw'>=</span> <span class='no'>m_fomc_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='kw'>=</span> <span class='no'>m_dfop_sfo</span>), <span class='no'>ds_2</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>]) <span class='co'># Separate fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>]) <span class='co'># Separate fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) <span class='co'># plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures</span> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># Global mixed model: Fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># Global mixed model: Fits for datasets 3 and 4</span></div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># With formation fractions</span> <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># chi2 different due to different df attribution</span></div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span>:<span class='fl'>4</span>) <span class='co'># chi2 different due to different df attribution</span></div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># For more parameters, we need to increase pnlsMaxIter and the tolerance</span> <span class='co'># to get convergence</span> <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ], <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -394.1603, nlminb iterations: 2 +#> LME step: Loglik: -394.1603, nlminb iterations: 3 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.2079984 0.8563873 1.7454146 1.0917723 1.2756924 +#> -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8786 -#> fixed effects: 94.17379 -5.473199 -0.6970239 -0.2025094 2.103883 +#> PNLS step: RSS = 643.8803 +#> fixed effects: 94.17379 -5.473193 -0.6970236 -0.2025091 2.103883 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 0.7865373 0.1448077 +#> 0.7960134 0.1447728 #> #> **Iteration 2 #> LME step: Loglik: -396.3824, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -1.712408e-01 -2.680989e-05 1.842119e+00 1.073975e+00 1.322924e+00 +#> -1.712404e-01 -2.432655e-05 1.842120e+00 1.073975e+00 1.322925e+00 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.8022 -#> fixed effects: 94.17385 -5.473491 -0.6970405 -0.202514 2.103871 +#> PNLS step: RSS = 643.8035 +#> fixed effects: 94.17385 -5.473487 -0.6970404 -0.2025137 2.103871 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 5.341904e-05 1.227073e-03 +#> 5.382757e-05 1.236667e-03 #> #> **Iteration 3 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 -#> -0.1712484347 -0.0001513555 1.8420964843 1.0739800649 1.3229176990 +#> -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7947 -#> fixed effects: 94.17386 -5.473522 -0.6970423 -0.2025142 2.10387 +#> PNLS step: RSS = 643.7948 +#> fixed effects: 94.17386 -5.473521 -0.6970422 -0.2025144 2.10387 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 5.568186e-06 1.276609e-04 +#> 6.072817e-06 1.400857e-04 #> #> **Iteration 4 #> LME step: Loglik: -396.3825, nlminb iterations: 7 #> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 -#> -0.171251200 -0.000164506 1.842095097 1.073980200 1.322916184 +#> ds1 ds2 ds3 ds4 ds5 +#> -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 643.7934 +#> PNLS step: RSS = 643.7936 #> fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869 #> iterations: 100 #> Convergence crit. (must all become <= tolerance = 0.0001): #> fixed reStruct -#> 2.332100e-06 1.979007e-05 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ], +#> 1.027451e-06 2.275704e-05 </div><div class='input'> <span class='no'>f_nlme_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ], <span class='kw'>control</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>pnlsMaxIter</span> <span class='kw'>=</span> <span class='fl'>120</span>, <span class='kw'>tolerance</span> <span class='kw'>=</span> <span class='fl'>5e-4</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -404.9591, nlminb iterations: 1 +#> LME step: Loglik: -404.9582, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114594 0.9798456 1.6990016 0.7293119 0.3353829 1.7112922 +#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.391 -#> fixed effects: 93.82265 -5.455841 -0.6788837 -1.862191 -4.199654 0.05531046 +#> PNLS step: RSS = 630.3644 +#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7872619 0.5811683 +#> 0.7885368 0.5822683 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371222832 0.003084754 1.789952290 0.724634064 0.301559136 1.754244638 -#> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.359 -#> fixed effects: 93.82269 -5.456014 -0.6788967 -1.862202 -4.199678 0.05534118 -#> iterations: 120 -#> Convergence crit. (must all become <= tolerance = 0.0005): -#> fixed reStruct -#> 0.0005550885 0.0007749418 -#> -#> **Iteration 3 -#> LME step: Loglik: -407.7756, nlminb iterations: 11 -#> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371217033 0.003064156 1.789935045 0.724683005 0.301622307 1.754234135 +#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.358 -#> fixed effects: 93.82269 -5.456017 -0.6788969 -1.862197 -4.199677 0.05532978 +#> PNLS step: RSS = 630.3633 +#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 2.059533e-04 4.860085e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'> +#> 4.789774e-07 2.200661e-05 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8541 884.6194 -408.9270 -#> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33913 <.0001 -#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4042 -533.5910 2 vs 3 270.66712 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8541 884.6194 -408.927 -#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4042 -533.591 1 vs 2 249.328 <.0001</div><div class='input'> +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33975 <.0001 +#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716 <.0001</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_dfop_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>) <span class='co'># if we ignore FOMC</span></div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> $ff #> parent_sink parent_A1 A1_sink -#> 0.5912435 0.4087565 1.0000000 +#> 0.5912432 0.4087568 1.0000000 #> #> $distimes -#> DT50 DT90 -#> parent 19.13517 63.56565 -#> A1 66.02149 219.31865 +#> DT50 DT90 +#> parent 19.13518 63.5657 +#> A1 66.02155 219.3189 #> </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme_dfop_sfo</span>)</div><div class='output co'>#> $ff -#> parent_A1 parent_sink A1_sink -#> 0.2768571 0.7231429 1.0000000 +#> parent_A1 parent_sink +#> 0.2768574 0.7231426 #> #> $distimes -#> DT50 DT90 DT50_k1 DT50_k2 -#> parent 11.07092 104.6325 4.462389 46.2085 -#> A1 162.30937 539.1801 NA NA +#> DT50 DT90 DT50_k1 DT50_k2 +#> parent 11.07091 104.6320 4.462384 46.20825 +#> A1 162.30536 539.1667 NA NA #> </div><div class='input'># } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#see-also">See also</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <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> @@ -455,7 +445,7 @@ parameters taken from the mmkin object are used</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 2ede2dec..284c30a6 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -74,7 +74,7 @@ observed data together with the solution of the fitted model." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -255,7 +255,7 @@ fits is shown, the residual plot is in the lower third of the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. If this is set to 'standardized', a plot of the residuals divided by the standard deviation - given by the fitted error model will be shown.</p></td> +given by the fitted error model will be shown.</p></td> </tr> <tr> <th>show_errplot</th> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef5718e5..4b893032 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -11,23 +11,27 @@ of an mmkin object — plot.mmkin • mkin</title> <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -41,7 +45,6 @@ of an mmkin object — plot.mmkin" /> <meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), 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." /> -<meta name="twitter:card" content="summary" /> @@ -59,7 +62,7 @@ the fit of at least one model to the same dataset is shown." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ the fit of at least one model to the same dataset is shown." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -133,7 +141,7 @@ the fit of at least one model to the same dataset is shown." /> <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='http://github.com/jranke/mkin/blob/master/R/plot.mmkin.R'><code>R/plot.mmkin.R</code></a></small> <div class="hidden name"><code>plot.mmkin.Rd</code></div> </div> @@ -144,7 +152,7 @@ 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.html'>plot</a></span>( +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( <span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, @@ -185,7 +193,7 @@ values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot <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 -`resplot = "time"`.</p></td> +<code>resplot = "time"</code>.</p></td> </tr> <tr> <th>show_errmin</th> @@ -237,27 +245,20 @@ latex is being used for the formatting of the chi2 error level.</p> <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span> <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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.html'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</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.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</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.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'> +#> <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</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/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</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/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>FALSE</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.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</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='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</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.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> # } + <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ], <span class='kw'>resplot</span> <span class='kw'>=</span> <span class='st'>"errmod"</span>)</div><div class='img'><img src='plot.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'> # } </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -268,7 +269,7 @@ latex is being used for the formatting of the chi2 error level.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/plot.nlme.mmkin-2.png b/docs/reference/plot.nlme.mmkin-2.png Binary files differindex 27c09796..265fd2e0 100644 --- a/docs/reference/plot.nlme.mmkin-2.png +++ b/docs/reference/plot.nlme.mmkin-2.png diff --git a/docs/reference/plot.nlme.mmkin.html b/docs/reference/plot.nlme.mmkin.html index 256739eb..9c85fbf0 100644 --- a/docs/reference/plot.nlme.mmkin.html +++ b/docs/reference/plot.nlme.mmkin.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -37,7 +41,6 @@ <meta property="og:title" content="Plot a fitted nonlinear mixed model obtained via an mmkin row object — plot.nlme.mmkin" /> <meta property="og:description" content="Plot a fitted nonlinear mixed model obtained via an mmkin row object" /> -<meta name="twitter:card" content="summary" /> @@ -55,7 +58,7 @@ </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -69,7 +72,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -113,7 +116,12 @@ </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -128,7 +136,7 @@ <div class="col-md-9 contents"> <div class="page-header"> <h1>Plot a fitted nonlinear mixed model obtained via an mmkin row object</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/plot.nlme.mmkin.R'><code>R/plot.nlme.mmkin.R</code></a></small> <div class="hidden name"><code>plot.nlme.mmkin.Rd</code></div> </div> @@ -137,7 +145,7 @@ </div> <pre class="usage"><span class='co'># S3 method for nlme.mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>( +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>( <span class='no'>x</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span>(<span class='no'>x</span>$<span class='no'>mmkin_orig</span>), <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, @@ -183,7 +191,7 @@ values, with the error model, using <code><a href='mkinerrplot.html'>mkinerrplot <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 -`resplot = "time"`.</p></td> +<code>resplot = "time"</code>.</p></td> </tr> <tr> <th>show_errmin</th> @@ -229,22 +237,16 @@ than two rows of plots are shown.</p></td> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)], <span class='no'>name</span> <span class='kw'>==</span> <span class='st'>"parent"</span>)) <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='co'>#plot(f) # too many panels for pkgdown</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f</span>[, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f</span>[, <span class='fl'>3</span>:<span class='fl'>4</span>])</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) <span class='no'>f_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>) <span class='co'>#plot(f_nlme) # too many panels for pkgdown</span> -<span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre> +<span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='no'>f_nlme</span>, <span class='fl'>3</span>:<span class='fl'>4</span>)</div><div class='img'><img src='plot.nlme.mmkin-2.png' alt='' width='700' height='433' /></div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -255,7 +257,7 @@ than two rows of plots are shown.</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html index 1795e6c3..76e2eb8f 100644 --- a/docs/reference/sigma_twocomp.html +++ b/docs/reference/sigma_twocomp.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -38,7 +42,6 @@ <meta property="og:title" content="Two-component error model — sigma_twocomp" /> <meta property="og:description" content="Function describing the standard deviation of the measurement error in dependence of the measured value \(y\):" /> -<meta name="twitter:card" content="summary" /> @@ -56,7 +59,7 @@ dependence of the measured value \(y\):" /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -70,7 +73,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -114,7 +117,12 @@ dependence of the measured value \(y\):" /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -129,7 +137,7 @@ dependence of the measured value \(y\):" /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Two-component error model</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/sigma_twocomp.R'><code>R/sigma_twocomp.R</code></a></small> <div class="hidden name"><code>sigma_twocomp.Rd</code></div> </div> @@ -173,21 +181,16 @@ y.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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> +Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry +24(11), 1895-1898.</p> <p>Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> +measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#references">References</a></li> - </ul> - + <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> @@ -198,7 +201,7 @@ y.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index ec79c37d..84e65787 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -41,7 +45,6 @@ some uncertainty statistics, the chi2 error levels calculated according to FOCUS guidance (2006) as defined therein, formation fractions, DT50 values and optionally the data, consisting of observed, predicted and residual values." /> -<meta name="twitter:card" content="summary" /> @@ -59,7 +62,7 @@ values." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -73,7 +76,7 @@ values." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -117,7 +120,12 @@ values." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -132,7 +140,7 @@ values." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Summary method for class "mkinfit"</h1> - + <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/summary.mkinfit.R'><code>R/summary.mkinfit.R</code></a></small> <div class="hidden name"><code>summary.mkinfit.Rd</code></div> </div> @@ -190,96 +198,97 @@ distribution</p></td> <p>The summary function returns a list with components, among others</p> <dt>version, Rversion</dt><dd><p>The mkin and R versions used</p></dd> - <dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were - produced</p></dd> - <dt>diffs</dt><dd><p>The differential equations used in the model</p></dd> - <dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> - <dt>bpar</dt><dd><p>Optimised and backtransformed - parameters</p></dd> - <dt>data</dt><dd><p>The data (see Description above).</p></dd> - <dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised - parameters.</p></dd> - <dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd> - <dt>errmin </dt><dd><p>The chi2 error levels for - each observed variable.</p></dd> - <dt>bparms.ode</dt><dd><p>All backtransformed ODE - parameters, for use as starting parameters for related models.</p></dd> - <dt>errparms</dt><dd><p>Error model parameters.</p></dd> - <dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted - model.</p></dd> - <dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> - <dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> - The print method is called for its side effect, i.e. printing the summary. +<dt>date.fit, date.summary</dt><dd><p>The dates where the fit and the summary were +produced</p></dd> +<dt>diffs</dt><dd><p>The differential equations used in the model</p></dd> +<dt>use_of_ff</dt><dd><p>Was maximum or minimum use made of formation fractions</p></dd> +<dt>bpar</dt><dd><p>Optimised and backtransformed +parameters</p></dd> +<dt>data</dt><dd><p>The data (see Description above).</p></dd> +<dt>start</dt><dd><p>The starting values and bounds, if applicable, for optimised +parameters.</p></dd> +<dt>fixed</dt><dd><p>The values of fixed parameters.</p></dd> +<dt>errmin </dt><dd><p>The chi2 error levels for +each observed variable.</p></dd> +<dt>bparms.ode</dt><dd><p>All backtransformed ODE +parameters, for use as starting parameters for related models.</p></dd> +<dt>errparms</dt><dd><p>Error model parameters.</p></dd> +<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted +model.</p></dd> +<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd> +<dt>SFORB</dt><dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd> +The print method is called for its side effect, i.e. printing the summary. <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>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 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> +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +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="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.9 -#> R version used for fitting: 3.6.3 -#> Date of fit: Mon Mar 30 21:43:00 2020 -#> Date of summary: Mon Mar 30 21:43:00 2020 + <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.50.1 +#> R version used for fitting: 4.0.0 +#> Date of fit: Tue May 12 08:07:03 2020 +#> Date of summary: Tue May 12 08:07:03 2020 #> #> Equations: -#> d_parent/dt = - k_parent_sink * parent +#> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.306 s +#> Fitted using 131 model solutions performed in 0.026 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 101.24 state -#> k_parent_sink 0.10 deparm +#> value type +#> parent_0 101.24 state +#> k_parent 0.10 deparm #> #> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 101.240000 -Inf Inf -#> log_k_parent_sink -2.302585 -Inf Inf +#> value lower upper +#> parent_0 101.240000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf #> #> Fixed parameter values: #> None #> +#> Results: +#> +#> AIC BIC logLik +#> 55.28197 55.5203 -24.64099 +#> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 109.200 3.70400 99.630 118.700 -#> log_k_parent_sink -3.291 0.09176 -3.527 -3.055 -#> sigma 5.266 1.31600 1.882 8.649 +#> Estimate Std. Error Lower Upper +#> parent_0 109.200 3.70400 99.630 118.700 +#> log_k_parent -3.291 0.09176 -3.527 -3.055 +#> sigma 5.266 1.31600 1.882 8.649 #> #> Parameter correlation: -#> parent_0 log_k_parent_sink sigma -#> parent_0 1.000e+00 5.428e-01 1.642e-07 -#> log_k_parent_sink 5.428e-01 1.000e+00 2.507e-07 -#> sigma 1.642e-07 2.507e-07 1.000e+00 +#> parent_0 log_k_parent sigma +#> parent_0 1.000e+00 5.428e-01 1.642e-07 +#> log_k_parent 5.428e-01 1.000e+00 2.507e-07 +#> sigma 1.642e-07 2.507e-07 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_0 109.20000 29.47 4.218e-07 99.6300 118.70000 -#> k_parent_sink 0.03722 10.90 5.650e-05 0.0294 0.04712 -#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000 +#> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712 +#> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 8.385 2 6 #> parent 8.385 2 6 #> -#> Resulting formation fractions: -#> ff -#> parent_sink 1 -#> #> Estimated disappearance times: #> DT50 DT90 #> parent 18.62 61.87 @@ -296,17 +305,10 @@ distribution</p></td> #> 118 parent 0.39 1.351 -0.9613</div><div class='input'> </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -317,7 +319,7 @@ distribution</p></td> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 2a08228d..fc0ffef2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -10,23 +10,27 @@ <!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> +<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/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> +<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/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> +<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/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> +<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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> +<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/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> +<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"> @@ -42,7 +46,6 @@ constants and other paramters 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="twitter:card" content="summary" /> @@ -60,7 +63,7 @@ the ilr transformation is used." /> </head> - <body> + <body data-spy="scroll" data-target="#toc"> <div class="container template-reference-topic"> <header> <div class="navbar navbar-default navbar-fixed-top" role="navigation"> @@ -74,7 +77,7 @@ the ilr transformation is used." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span> </span> </div> @@ -118,7 +121,12 @@ the ilr transformation is used." /> </li> </ul> <ul class="nav navbar-nav navbar-right"> - + <li> + <a href="http://github.com/jranke/mkin/"> + <span class="fab fa fab fa-github fa-lg"></span> + + </a> +</li> </ul> </div><!--/.nav-collapse --> @@ -133,7 +141,7 @@ the ilr transformation is used." /> <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='http://github.com/jranke/mkin/blob/master/R/transform_odeparms.R'><code>R/transform_odeparms.R</code></a></small> <div class="hidden name"><code>transform_odeparms.Rd</code></div> </div> @@ -204,7 +212,7 @@ fitting procedure.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>A vector of transformed or backtransformed parameters with the same - names as the original parameters.</p> +names as the original parameters.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <p>The transformation of sets of formation fractions is fragile, as it supposes @@ -224,39 +232,28 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit< <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</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='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.60 1.5702 96.40 102.79 -#> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 -#> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 -#> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 -#> sigma 3.13 0.3585 2.40 3.85</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</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='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper +#> parent_0 99.598 1.5702 96.4038 102.793 +#> log_k_parent -2.316 0.0409 -2.3988 -2.233 +#> log_k_m1 -5.248 0.1332 -5.5184 -4.977 +#> f_parent_ilr_1 0.041 0.0631 -0.0875 0.169 +#> sigma 3.126 0.3585 2.3961 3.855</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</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 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='co'># \dontrun{</span> <span class='co'># Compare to the version without transforming rate parameters</span> -<span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>) -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> Estimate Std. Error Lower Upper -#> parent_0 99.59848 1.57022 96.40384 1.03e+02 -#> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 -#> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 -#> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 -#> sigma 3.12550 0.35852 2.39609 3.85e+00</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</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='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='error'>Error in if (cost < cost.current) { assign("cost.current", cost, inherits = TRUE) if (!quiet) cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"), " at call ", calls, ": ", cost.current, "\n", sep = "")}: Fehlender Wert, wo TRUE/FALSE nötig ist</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.002 0 0.003</span></div><div class='input'><span class='no'>fit.2.s</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit.2</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.2): Objekt 'fit.2' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>par</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$par, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>fit.2.s</span>$<span class='no'>bpar</span>, <span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in print(fit.2.s$bpar, 3): Objekt 'fit.2.s' nicht gefunden</span></div><div class='input'><span class='co'># }</span> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>) <span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/colnames.html'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) -<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</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='no'>transformed</span>, <span class='no'>SFO_SFO</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='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> 100.750000 -2.302585 -2.301586 0.000000 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent k_m1 f_parent_to_m1 +#> 100.7500 0.1000 0.1001 0.5000 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># The case of formation fractions</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( @@ -297,18 +294,10 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit< </div></pre> </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - <li><a href="#arguments">Arguments</a></li> - <li><a href="#value">Value</a></li> - <li><a href="#details">Details</a></li> - <li><a href="#functions">Functions</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - - <h2>Author</h2> - <p>Johannes Ranke</p> + <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> @@ -319,7 +308,7 @@ This is no problem for the internal use in <code><a href='mkinfit.html'>mkinfit< </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> </div> </footer> diff --git a/dumpdata.R b/dumpdata.R new file mode 100644 index 00000000..881df526 --- /dev/null +++ b/dumpdata.R @@ -0,0 +1,7 @@ +mkinpredict <- +function (x, odeparms, odeini, outtimes = seq(0, 120, by = 0.10000000000000001), + solution_type = "deSolve", use_compiled = "auto", method.ode = "lsoda", + atol = 1e-08, rtol = 1e-10, map_output = TRUE, ...) +{ + UseMethod("mkinpredict", x) +} diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd index a10d0aeb..13081561 100644 --- a/man/AIC.mmkin.Rd +++ b/man/AIC.mmkin.Rd @@ -19,7 +19,7 @@ column.} } \value{ As in the generic method (a numeric value for single fits, or a - dataframe if there are several fits in the column). +dataframe if there are several fits in the column). } \description{ Provides a convenient way to compare different kinetic models fitted to the diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd index 8ada60c5..d8c4553e 100644 --- a/man/DFOP.solution.Rd +++ b/man/DFOP.solution.Rd @@ -32,15 +32,15 @@ two exponential decline functions. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd index e5e46c87..eeee85f9 100644 --- a/man/FOMC.solution.Rd +++ b/man/FOMC.solution.Rd @@ -30,8 +30,8 @@ in the original equation. } \note{ The solution of the FOMC kinetic model reduces to the - \code{\link{SFO.solution}} for large values of \code{alpha} and - \code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. +\code{\link{SFO.solution}} for large values of \code{alpha} and +\code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. } \examples{ @@ -40,20 +40,20 @@ The solution of the FOMC kinetic model reduces to the } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: - A new model based on spatial variability. \emph{Environmental Science and - Technology} \bold{24}, 1032-1038 +Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: +A new model based on spatial variability. \emph{Environmental Science and +Technology} \bold{24}, 1032-1038 } \seealso{ Other parent solutions: diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd index f72df23b..2940e949 100644 --- a/man/HS.solution.Rd +++ b/man/HS.solution.Rd @@ -33,15 +33,15 @@ between them. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd index e1f1be1a..1150f023 100644 --- a/man/IORE.solution.Rd +++ b/man/IORE.solution.Rd @@ -25,9 +25,9 @@ a concentration dependent rate constant. } \note{ The solution of the IORE kinetic model reduces to the - \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can - be transformed to equivalent parameters of the FOMC mode - see the NAFTA - guidance for details. +\code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can +be transformed to equivalent parameters of the FOMC mode - see the NAFTA +guidance for details. } \examples{ @@ -46,7 +46,7 @@ The solution of the IORE kinetic model reduces to the } \references{ NAFTA Technical Working Group on Pesticides (not dated) Guidance - for Evaluating and Calculating Degradation Kinetics in Environmental Media +for Evaluating and Calculating Degradation Kinetics in Environmental Media } \seealso{ Other parent solutions: diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd index 6892cccc..c0aac237 100644 --- a/man/SFO.solution.Rd +++ b/man/SFO.solution.Rd @@ -26,15 +26,15 @@ Function describing exponential decline from a defined starting value. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd index 98a8c684..dc78d1f1 100644 --- a/man/SFORB.solution.Rd +++ b/man/SFORB.solution.Rd @@ -20,7 +20,7 @@ fraction.} } \value{ The value of the response variable, which is the sum of free and - bound fractions at time \code{t}. +bound fractions at time \code{t}. } \description{ Function describing the solution of the differential equations describing @@ -36,15 +36,15 @@ and no substance in the bound fraction. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/add_err.Rd b/man/add_err.Rd index 3452923e..1171e0fd 100644 --- a/man/add_err.Rd +++ b/man/add_err.Rd @@ -40,7 +40,7 @@ seed is not set.} } \value{ A list of datasets compatible with \code{\link{mmkin}}, i.e. the - components of the list are datasets compatible with \code{\link{mkinfit}}. +components of the list are datasets compatible with \code{\link{mkinfit}}. } \description{ Normally distributed errors are added to data predicted for a specific diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd index 81d7a6e8..f295afc4 100644 --- a/man/confint.mkinfit.Rd +++ b/man/confint.mkinfit.Rd @@ -45,7 +45,7 @@ applied to the likelihood based on the transformed parameters?} transformed parameters, should we backtransform the parameters with their confidence intervals?} -\item{cores}{The number of cores to be used for multicore processing. +\item{cores}{The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.} \item{quiet}{Should we suppress the message "Profiling the likelihood"} @@ -54,7 +54,7 @@ On Windows machines, cores > 1 is currently not supported.} } \value{ A matrix with columns giving lower and upper confidence limits for - each parameter. +each parameter. } \description{ The default method 'quadratic' is based on the quadratic approximation of @@ -143,10 +143,10 @@ confint(f_tc_2, "parent_0", method = "quadratic") \references{ Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications - Pawitan Y (2013) In all likelihood - Statistical modelling and - inference using likelihood. Clarendon Press, Oxford. +Pawitan Y (2013) In all likelihood - Statistical modelling and +inference using likelihood. Clarendon Press, Oxford. - Venzon DJ and Moolgavkar SH (1988) A Method for Computing - Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, - 87–94. +Venzon DJ and Moolgavkar SH (1988) A Method for Computing +Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, +87–94. } diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 26b5ee08..49f44d74 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -13,9 +13,9 @@ endpoints(fit) } \value{ A list with a matrix of dissipation times named distimes, - and, if applicable, a vector of formation fractions named ff - and, if the SFORB model was in use, a vector of eigenvalues - of these SFORB models, equivalent to DFOP rate constants +and, if applicable, a vector of formation fractions named ff +and, if the SFORB model was in use, a vector of eigenvalues +of these SFORB models, equivalent to DFOP rate constants } \description{ This function calculates DT50 and DT90 values as well as formation fractions diff --git a/man/get_deg_func.Rd b/man/get_deg_func.Rd index 1d8a3de9..75743448 100644 --- a/man/get_deg_func.Rd +++ b/man/get_deg_func.Rd @@ -8,7 +8,7 @@ get_deg_func() } \value{ A function that was likely previously assigned from within - nlme.mmkin +nlme.mmkin } \description{ Retrieve a degradation function from the mmkin namespace @@ -15,8 +15,8 @@ sensible for vectors with all elements being greater than zero.} } \value{ The result of the forward or backward transformation. The returned - components always sum to 1 for the case of the inverse log-ratio - transformation. +components always sum to 1 for the case of the inverse log-ratio +transformation. } \description{ This implementation is a special case of the class of isometric log-ratio @@ -48,11 +48,11 @@ ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5) } \references{ Peter Filzmoser, Karel Hron (2008) Outlier Detection for - Compositional Data Using Robust Methods. Math Geosci 40 233-248 +Compositional Data Using Robust Methods. Math Geosci 40 233-248 } \seealso{ Another implementation can be found in R package - \code{robCompositions}. +\code{robCompositions}. } \author{ René Lehmann and Johannes Ranke diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index 502fb4d7..637570e4 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -13,8 +13,8 @@ } \value{ An object of class \code{\link{logLik}} with the number of estimated - parameters (degradation model parameters plus variance model parameters) - as attribute. +parameters (degradation model parameters plus variance model parameters) +as attribute. } \description{ This function returns the product of the likelihood densities of each @@ -45,7 +45,7 @@ and the fitted error model parameters. } \seealso{ Compare the AIC of columns of \code{\link{mmkin}} objects using - \code{\link{AIC.mmkin}}. +\code{\link{AIC.mmkin}}. } \author{ Johannes Ranke diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd index 33b3d44a..efa12e7a 100644 --- a/man/logistic.solution.Rd +++ b/man/logistic.solution.Rd @@ -26,7 +26,7 @@ an increasing rate constant, supposedly caused by microbial growth } \note{ The solution of the logistic model reduces to the - \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. +\code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. } \examples{ @@ -67,15 +67,15 @@ The solution of the logistic model reduces to the } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{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, - Version 1.1, 18 December 2014 - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +Version 1.1, 18 December 2014 +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \seealso{ Other parent solutions: diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd index 7c9f4861..107eebd0 100644 --- a/man/max_twa_parent.Rd +++ b/man/max_twa_parent.Rd @@ -48,8 +48,8 @@ factor (f_twa) is calculated.} } \value{ For \code{max_twa_parent}, a numeric vector, named using the - \code{windows} argument. For the other functions, a numeric vector of - length one (also known as 'a number'). +\code{windows} argument. For the other functions, a numeric vector of +length one (also known as 'a number'). } \description{ This function calculates maximum moving window time weighted average @@ -66,10 +66,10 @@ soil section of the FOCUS guidance. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd index 9564ec19..82178aa9 100644 --- a/man/mkinerrplot.Rd +++ b/man/mkinerrplot.Rd @@ -50,7 +50,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the squared residuals for the specified subset of the @@ -70,7 +70,7 @@ mkinerrplot(fit) } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object. +lines of the mkinfit object. } \author{ Johannes Ranke diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index db3f5f3e..97dffef7 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -3,10 +3,6 @@ \name{mkinfit} \alias{mkinfit} \title{Fit a kinetic model to data with one or more state variables} -\source{ -Rocke, David M. und Lorenzato, Stefan (1995) A two-component model - for measurement error in analytical chemistry. Technometrics 37(2), 176-184. -} \usage{ mkinfit( mkinmod, @@ -53,16 +49,16 @@ not observed in degradation data, because there is a lower limit of detection.} \item{parms.ini}{A named vector of initial values for the parameters, - including parameters to be optimised and potentially also fixed parameters - as indicated by \code{fixed_parms}. If set to "auto", initial values for - rate constants are set to default values. Using parameter names that are - not in the model gives an error. +including parameters to be optimised and potentially also fixed parameters +as indicated by \code{fixed_parms}. If set to "auto", initial values for +rate constants are set to default values. Using parameter names that are +not in the model gives an error. - It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from - this model. This works nicely if the models are nested. An example is - given below.} +It is possible to only specify a subset of the parameters that the model +needs. You can use the parameter lists "bparms.ode" from a previously +fitted model, which contains the differential equation parameters from +this model. This works nicely if the models are nested. An example is +given below.} \item{state.ini}{A named vector of initial values for the state variables of the model. In case the observed variables are represented by more than one @@ -141,48 +137,50 @@ is 1e-8, lower than in \code{\link{lsoda}}.} is 1e-10, much lower than in \code{\link{lsoda}}.} \item{error_model}{If the error model is "const", a constant standard - deviation is assumed. +deviation is assumed. - If the error model is "obs", each observed variable is assumed to have its - own variance. +If the error model is "obs", each observed variable is assumed to have its +own variance. - If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model - deviates from the model by Rocke and Lorenzato, as their model implies - that the errors follow a lognormal distribution for large values, not a - normal distribution as assumed by this method.} +If the error model is "tc" (two-component error model), a two component +error model similar to the one described by Rocke and Lorenzato (1995) is +used for setting up the likelihood function. Note that this model +deviates from the model by Rocke and Lorenzato, as their model implies +that the errors follow a lognormal distribution for large values, not a +normal distribution as assumed by this method.} \item{error_model_algorithm}{If "auto", the selected algorithm depends on - the error model. If the error model is "const", unweighted nonlinear - least squares fitting ("OLS") is selected. If the error model is "obs", or - "tc", the "d_3" algorithm is selected. - - The algorithm "d_3" will directly minimize the negative log-likelihood and - - independently - also use the three step algorithm described below. The - fit with the higher likelihood is returned. +the error model. If the error model is "const", unweighted nonlinear +least squares fitting ("OLS") is selected. If the error model is "obs", or +"tc", the "d_3" algorithm is selected. + +The algorithm "d_3" will directly minimize the negative log-likelihood and +\itemize{ +\item independently - also use the three step algorithm described below. The +fit with the higher likelihood is returned. +} - The algorithm "direct" will directly minimize the negative log-likelihood. +The algorithm "direct" will directly minimize the negative log-likelihood. - The algorithm "twostep" will minimize the negative log-likelihood after an - initial unweighted least squares optimisation step. +The algorithm "twostep" will minimize the negative log-likelihood after an +initial unweighted least squares optimisation step. - The algorithm "threestep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, and then minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "threestep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, and then minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "fourstep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, then optimizes the degradation model again with fixed error model - parameters, and finally minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "fourstep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, then optimizes the degradation model again with fixed error model +parameters, and finally minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error - model parameters and subsequent optimization of the degradation model - using those error model parameters, until the error model parameters - converge.} +The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with +unweighted least squares, and then iterates optimization of the error +model parameters and subsequent optimization of the degradation model +using those error model parameters, until the error model parameters +converge.} \item{reweight.tol}{Tolerance for the convergence criterion calculated from the error model parameters in IRLS fits.} @@ -196,7 +194,7 @@ the error model parameters in IRLS fits.} } \value{ A list with "mkinfit" in the class attribute. A summary can be - obtained by \code{\link{summary.mkinfit}}. +obtained by \code{\link{summary.mkinfit}}. } \description{ This function maximises the likelihood of the observed data using the Port @@ -214,9 +212,9 @@ estimators. } \note{ When using the "IORE" submodel for metabolites, fitting with - "transform_rates = TRUE" (the default) often leads to failures of the - numerical ODE solver. In this situation it may help to switch off the - internal rate transformation. +"transform_rates = TRUE" (the default) often leads to failures of the +numerical ODE solver. In this situation it may help to switch off the +internal rate transformation. } \examples{ @@ -268,7 +266,7 @@ fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.o } \dontrun{ -# Weighted fits, including IRLS +# Weighted fits, including IRLS (error_model = "obs") SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max") f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) @@ -281,15 +279,23 @@ summary(f.tc) } +\references{ +Rocke DM and Lorenzato S (1995) A two-component model +for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184. + +Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. \emph{Environments} 6(12) 124 +\href{https://doi.org/10.3390/environments6120124}{doi:10.3390/environments6120124}. +} \seealso{ Plotting methods \code{\link{plot.mkinfit}} and - \code{\link{mkinparplot}}. +\code{\link{mkinparplot}}. - Comparisons of models fitted to the same data can be made using - \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. +Comparisons of models fitted to the same data can be made using +\code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. - Fitting of several models to several datasets in a single call to - \code{\link{mmkin}}. +Fitting of several models to several datasets in a single call to +\code{\link{mmkin}}. } \author{ Johannes Ranke diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index a5736be7..6a6d2027 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -44,25 +44,30 @@ applicable to give detailed information about the C function being built.} } \value{ A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, - containing, among others, - \item{diffs}{ - A vector of string representations of differential equations, one for - each modelling variable. - } - \item{map}{ - A list containing named character vectors for each observed variable, - specifying the modelling variables by which it is represented. - } - \item{use_of_ff}{ - The content of \code{use_of_ff} is passed on in this list component. - } - \item{coefmat}{ - The coefficient matrix, if the system of differential equations can be - represented by one. - } - \item{cf}{ - If generated, the compiled function as returned by cfunction. - } +containing, among others, +\item{diffs}{ +A vector of string representations of differential equations, one for +each modelling variable. +} +\item{map}{ +A list containing named character vectors for each observed variable, +specifying the modelling variables by which it is represented. +} +\item{use_of_ff}{ +The content of \code{use_of_ff} is passed on in this list component. +} +\item{deg_func}{ +If generated, a function containing the solution of the degradation +model. +} +\item{coefmat}{ +The coefficient matrix, if the system of differential equations can be +represented by one. +} +\item{cf}{ +If generated, a compiled function calculating the derivatives as +returned by cfunction. +} } \description{ The function usually takes several expressions, each assigning a compound @@ -76,8 +81,8 @@ in the FOCUS and NAFTA guidance documents are used. } \note{ The IORE submodel is not well tested for metabolites. When using this - model for metabolites, you may want to read the second note in the help - page to \code{\link{mkinfit}}. +model for metabolites, you may want to read the second note in the help +page to \code{\link{mkinfit}}. } \examples{ @@ -115,13 +120,13 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental Media +NAFTA Technical Working Group on Pesticides (not dated) Guidance for +Evaluating and Calculating Degradation Kinetics in Environmental Media } \author{ Johannes Ranke diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd index 975a0203..07b25009 100644 --- a/man/mkinparplot.Rd +++ b/man/mkinparplot.Rd @@ -11,7 +11,7 @@ mkinparplot(object) } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the confidence intervals for the parameters fitted using diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index 2a8b2d41..498d914d 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -54,7 +54,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the residuals for the specified subset of the observed @@ -71,8 +71,8 @@ mkinresplot(fit, "m1") } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object, and \code{\link{plot_res}} for a function - combining the plot of the fit and the residual plot. +lines of the mkinfit object, and \code{\link{plot_res}} for a function +combining the plot of the fit and the residual plot. } \author{ Johannes Ranke diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 99895400..eda0d837 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -33,8 +33,8 @@ for parallel execution.} } \value{ A two-dimensional \code{\link{array}} of \code{\link{mkinfit}} - objects that can be indexed using the model names for the first index (row index) - and the dataset names for the second index (column index). +objects that can be indexed using the model names for the first index (row index) +and the dataset names for the second index (column index). } \description{ This function calls \code{\link{mkinfit}} on all combinations of models and @@ -79,7 +79,7 @@ plot(fits.0[1, 1]) } \seealso{ \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for - plotting. +plotting. } \author{ Johannes Ranke diff --git a/man/nafta.Rd b/man/nafta.Rd index 49c13afc..4f05324b 100644 --- a/man/nafta.Rd +++ b/man/nafta.Rd @@ -6,15 +6,15 @@ \title{Evaluate parent kinetics using the NAFTA guidance} \source{ NAFTA (2011) Guidance for evaluating and calculating degradation - kinetics in environmental media. NAFTA Technical Working Group on - Pesticides - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} - accessed 2019-02-22 +kinetics in environmental media. NAFTA Technical Working Group on +Pesticides +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} +accessed 2019-02-22 - US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to - Calculate Representative Half-life Values and Characterizing Pesticide - Degradation - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} +US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to +Calculate Representative Half-life Values and Characterizing Pesticide +Degradation +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} } \usage{ nafta(ds, title = NA, quiet = FALSE, ...) @@ -41,9 +41,9 @@ dissipation times.} } \value{ An list of class \code{nafta}. The list element named "mmkin" is the - \code{\link{mmkin}} 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. +\code{\link{mmkin}} 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. } \description{ The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}} diff --git a/man/nlme.Rd b/man/nlme.Rd index a9e368dd..bf527320 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -21,9 +21,9 @@ nlme_data(object) A function that can be used with nlme If random is FALSE (default), a named vector containing mean values - of the fitted degradation model parameters. If random is TRUE, a list with - fixed and random effects, in the format required by the start argument of - nlme for the case of a single grouping variable ds? +of the fitted degradation model parameters. If random is TRUE, a list with +fixed and random effects, in the format required by the start argument of +nlme for the case of a single grouping variable ds? A \code{\link{groupedData}} object } diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 430dbda1..ae2b2d22 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -67,7 +67,7 @@ parameters taken from the mmkin object are used} } \value{ Upon success, a fitted nlme.mmkin object, which is an nlme object - with additional elements +with additional elements } \description{ This functions sets up a nonlinear mixed effects model for an mmkin row diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 4235557e..bf38c5a5 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -85,7 +85,7 @@ fits is shown, the residual plot is in the lower third of the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. If this is set to 'standardized', a plot of the residuals divided by the standard deviation - given by the fitted error model will be shown.} +given by the fitted error model will be shown.} \item{show_errplot}{Should squared residuals and the error model be shown? If only one plot of the fits is shown, this plot is in the lower third of diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 600881ea..998e25e1 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -34,7 +34,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 9bea7013..91130402 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -36,7 +36,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd index 0004144f..4e1f7c38 100644 --- a/man/sigma_twocomp.Rd +++ b/man/sigma_twocomp.Rd @@ -33,9 +33,9 @@ y. } \references{ Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) - Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry - 24(11), 1895-1898. +Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry +24(11), 1895-1898. - Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184. +Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for +measurement error in analytical chemistry. Technometrics 37(2), 176-184. } diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd index fabe31d0..24991d71 100644 --- a/man/summary.mkinfit.Rd +++ b/man/summary.mkinfit.Rd @@ -29,27 +29,27 @@ distribution} } \value{ The summary function returns a list with components, among others - \item{version, Rversion}{The mkin and R versions used} - \item{date.fit, date.summary}{The dates where the fit and the summary were - produced} - \item{diffs}{The differential equations used in the model} - \item{use_of_ff}{Was maximum or minimum use made of formation fractions} - \item{bpar}{Optimised and backtransformed - parameters} - \item{data}{The data (see Description above).} - \item{start}{The starting values and bounds, if applicable, for optimised - parameters.} - \item{fixed}{The values of fixed parameters.} - \item{errmin }{The chi2 error levels for - each observed variable.} - \item{bparms.ode}{All backtransformed ODE - parameters, for use as starting parameters for related models.} - \item{errparms}{Error model parameters.} - \item{ff}{The estimated formation fractions derived from the fitted - model.} - \item{distimes}{The DT50 and DT90 values for each observed variable.} - \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} - The print method is called for its side effect, i.e. printing the summary. +\item{version, Rversion}{The mkin and R versions used} +\item{date.fit, date.summary}{The dates where the fit and the summary were +produced} +\item{diffs}{The differential equations used in the model} +\item{use_of_ff}{Was maximum or minimum use made of formation fractions} +\item{bpar}{Optimised and backtransformed +parameters} +\item{data}{The data (see Description above).} +\item{start}{The starting values and bounds, if applicable, for optimised +parameters.} +\item{fixed}{The values of fixed parameters.} +\item{errmin }{The chi2 error levels for +each observed variable.} +\item{bparms.ode}{All backtransformed ODE +parameters, for use as starting parameters for related models.} +\item{errparms}{Error model parameters.} +\item{ff}{The estimated formation fractions derived from the fitted +model.} +\item{distimes}{The DT50 and DT90 values for each observed variable.} +\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} +The print method is called for its side effect, i.e. printing the summary. } \description{ Lists model equations, initial parameter values, optimised parameters with @@ -65,10 +65,10 @@ values. } \references{ FOCUS (2006) \dQuote{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 Document Reference Sanco/10058/2005 version 2.0, 434 pp, - \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +and Degradation Kinetics from Environmental Fate Studies on Pesticides in +EU Registration} Report of the FOCUS Work Group on Degradation Kinetics, +EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, +\url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 5257fe12..e250483a 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -48,7 +48,7 @@ fitting procedure.} } \value{ A vector of transformed or backtransformed parameters with the same - names as the original parameters. +names as the original parameters. } \description{ The transformations are intended to map parameters that should only take on |
