diff options
119 files changed, 3226 insertions, 489 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 916d1cdc..98fa4355 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.2.5 -Date: 2023-08-09 +Version: 1.2.6 +Date: 2023-08-10 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", @@ -1,3 +1,7 @@ +# mkin 1.2.6 + + + # mkin 1.2.5 - 'vignettes/mesotrione_parent_2023.rnw': Prebuilt vignette showing how covariate modelling can be done for all relevant parent degradation models. diff --git a/_pkgdown.yml b/_pkgdown.yml index f14e6ef3..996b8d3b 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,8 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: release - version_label: default + mode: devel + version_label: info template: bootswatch: spacelab diff --git a/docs/dev/articles/FOCUS_D.html b/docs/dev/articles/FOCUS_D.html index 4a9406de..ddfb268d 100644 --- a/docs/dev/articles/FOCUS_D.html +++ b/docs/dev/articles/FOCUS_D.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ D</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 31 January 2019 -(rebuilt 2023-04-16)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_D.rmd" class="external-link"><code>vignettes/FOCUS_D.rmd</code></a></small> <div class="hidden name"><code>FOCUS_D.rmd</code></div> @@ -238,10 +238,10 @@ the <code>mkinparplot</code> function.</p> <code>summary</code> method for <code>mkinfit</code> objects.</p> <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:12 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:12 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:10 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:10 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> diff --git a/docs/dev/articles/FOCUS_L.html b/docs/dev/articles/FOCUS_L.html index 853194fb..9500e661 100644 --- a/docs/dev/articles/FOCUS_L.html +++ b/docs/dev/articles/FOCUS_L.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -135,8 +135,8 @@ to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 18 May 2022 -(rebuilt 2023-04-16)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2023 +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/FOCUS_L.rmd" class="external-link"><code>vignettes/FOCUS_L.rmd</code></a></small> <div class="hidden name"><code>FOCUS_L.rmd</code></div> @@ -170,10 +170,10 @@ report.</p> <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L1.SFO</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_L1_mkin</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.SFO</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:11 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:11 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -277,10 +277,10 @@ objects.</p> <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> <span><span class="co">## is doubtful</span></span></code></pre> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> @@ -428,10 +428,10 @@ kinetics.</p> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:14 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:14 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> @@ -512,10 +512,10 @@ the data.</p> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> <div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:15 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:12 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:12 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -629,10 +629,10 @@ using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> <div class="sourceCode" id="cb24"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:15 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span></span> @@ -756,10 +756,10 @@ passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:16 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - k_parent * parent</span></span> @@ -821,10 +821,10 @@ appears negligible.</p> <span><span class="co">## parent 106 352</span></span></code></pre> <div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.3 </span></span> -<span><span class="co">## R version used for fitting: 4.2.3 </span></span> -<span><span class="co">## Date of fit: Sun Apr 16 08:35:15 2023 </span></span> -<span><span class="co">## Date of summary: Sun Apr 16 08:35:16 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> +<span><span class="co">## R version used for fitting: 4.3.0 </span></span> +<span><span class="co">## Date of fit: Fri May 19 17:34:13 2023 </span></span> +<span><span class="co">## Date of summary: Fri May 19 17:34:13 2023 </span></span> <span><span class="co">## </span></span> <span><span class="co">## Equations:</span></span> <span><span class="co">## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span></span> diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index c9116643..2ac74e53 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -111,7 +114,7 @@ <dd> </dd><dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt> <dd> - </dd><dt><a href="mkin.html">Introduction to mkin</a></dt> + </dd><dt><a href="mkin.html">Short introduction to mkin</a></dt> <dd> </dd><dt><a href="prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a></dt> <dd> @@ -119,6 +122,8 @@ <dd> </dd><dt><a href="prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a></dt> <dd> + </dd><dt><a href="prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a></dt> + <dd> </dd><dt><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></dt> <dd> </dd><dt><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></dt> diff --git a/docs/dev/articles/mkin.html b/docs/dev/articles/mkin.html index fa3ac11c..e0011a5a 100644 --- a/docs/dev/articles/mkin.html +++ b/docs/dev/articles/mkin.html @@ -5,13 +5,13 @@ <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Introduction to mkin • mkin</title> +<title>Short introduction to mkin • mkin</title> <!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"> <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"> <script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> +<script src="../pkgdown.js"></script><meta property="og:title" content="Short introduction to mkin"> <meta property="og:description" content="mkin"> <meta name="robots" content="noindex"> <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -130,12 +130,12 @@ </header><div class="row"> <div class="col-md-9 contents"> <div class="page-header toc-ignore"> - <h1 data-toc-skip>Introduction to mkin</h1> + <h1 data-toc-skip>Short introduction to mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">Last change 15 February 2021 -(rebuilt 2023-04-16)</h4> + <h4 data-toc-skip class="date">Last change 18 May 2023 +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/mkin.rmd" class="external-link"><code>vignettes/mkin.rmd</code></a></small> <div class="hidden name"><code>mkin.rmd</code></div> diff --git a/docs/dev/articles/prebuilt/2022_cyan_pathway.html b/docs/dev/articles/prebuilt/2022_cyan_pathway.html index 7bb0fa5b..2359969e 100644 --- a/docs/dev/articles/prebuilt/2022_cyan_pathway.html +++ b/docs/dev/articles/prebuilt/2022_cyan_pathway.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ residue data on cyantraniliprole</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_cyan_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_cyan_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_cyan_pathway.rmd</code></div> @@ -156,7 +156,7 @@ be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.4 which is currently under +<p>The mkin package is used in version 1.2.5 which is currently under development. The newly introduced functionality that is used here is a simplification of excluding random effects for a set of fits based on a related set of fits with a reduced model, and the documentation of the @@ -2220,10 +2220,10 @@ Hierarchical SFO path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:05 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:02 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2236,7 +2236,7 @@ Data: Model predictions using solution type deSolve -Fitted in 438.011 s +Fitted in 443.997 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2348,10 +2348,10 @@ Hierarchical SFO path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:32:55 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:01 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2364,7 +2364,7 @@ Data: Model predictions using solution type deSolve -Fitted in 427.249 s +Fitted in 442.545 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2478,10 +2478,10 @@ Hierarchical FOMC path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:49 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:38 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2496,7 +2496,7 @@ Data: Model predictions using solution type deSolve -Fitted in 481.497 s +Fitted in 479.463 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2623,10 +2623,10 @@ Hierarchical FOMC path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:33:59 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:42:53 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2641,7 +2641,7 @@ Data: Model predictions using solution type deSolve -Fitted in 491.071 s +Fitted in 494.121 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2761,10 +2761,10 @@ Hierarchical DFOP path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:22 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2783,7 +2783,7 @@ Data: Model predictions using solution type deSolve -Fitted in 525.551 s +Fitted in 523.691 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2907,10 +2907,10 @@ Hierarchical DFOP path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:37:03 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:46:08 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2929,7 +2929,7 @@ Data: Model predictions using solution type deSolve -Fitted in 675.804 s +Fitted in 689.217 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3053,10 +3053,10 @@ Hierarchical SFORB path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:43 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:37 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3074,7 +3074,7 @@ Data: Model predictions using solution type deSolve -Fitted in 535.818 s +Fitted in 538.025 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3218,10 +3218,10 @@ Hierarchical SFORB path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:37:02 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:45:51 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3239,7 +3239,7 @@ Data: Model predictions using solution type deSolve -Fitted in 674.859 s +Fitted in 672.309 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3383,10 +3383,10 @@ Hierarchical HS path 1 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:41 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:26 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3401,7 +3401,7 @@ Data: Model predictions using solution type deSolve -Fitted in 533.787 s +Fitted in 526.974 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3525,10 +3525,10 @@ Hierarchical HS path 1 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:34:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:43:29 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan @@ -3543,7 +3543,7 @@ Data: Model predictions using solution type deSolve -Fitted in 531.084 s +Fitted in 529.515 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3673,10 +3673,10 @@ Hierarchical FOMC path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:45:51 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:54:58 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3691,7 +3691,7 @@ Data: Model predictions using solution type deSolve -Fitted in 517.002 s +Fitted in 519.639 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3837,10 +3837,10 @@ Hierarchical FOMC path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:45:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:54:41 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3855,7 +3855,7 @@ Data: Model predictions using solution type deSolve -Fitted in 505.619 s +Fitted in 503.222 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3983,10 +3983,10 @@ Hierarchical DFOP path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:46:46 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:55:53 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4006,7 +4006,7 @@ Data: Model predictions using solution type deSolve -Fitted in 572.382 s +Fitted in 574.8 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4174,10 +4174,10 @@ Hierarchical DFOP path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:49:18 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:58:32 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4197,7 +4197,7 @@ Data: Model predictions using solution type deSolve -Fitted in 724.515 s +Fitted in 733.398 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4365,10 +4365,10 @@ Hierarchical SFORB path 2 fit with constant variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:46:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:55:51 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4386,7 +4386,7 @@ Data: Model predictions using solution type deSolve -Fitted in 559.097 s +Fitted in 572.747 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4561,10 +4561,10 @@ Hierarchical SFORB path 2 fit with two-component error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 20:49:20 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 17:58:21 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4582,7 +4582,7 @@ Data: Model predictions using solution type deSolve -Fitted in 726.293 s +Fitted in 722.847 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4762,10 +4762,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:02:39 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:12:10 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4780,7 +4780,7 @@ Data: Model predictions using solution type deSolve -Fitted in 796.615 s +Fitted in 816.454 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4905,10 +4905,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:15 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:38 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4928,7 +4928,7 @@ Data: Model predictions using solution type deSolve -Fitted in 893.328 s +Fitted in 904.25 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5071,10 +5071,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:33 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:00 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -5094,7 +5094,7 @@ Data: Model predictions using solution type deSolve -Fitted in 910.788 s +Fitted in 926.094 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5237,10 +5237,10 @@ variance </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:09 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:34 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5258,7 +5258,7 @@ Data: Model predictions using solution type deSolve -Fitted in 887.369 s +Fitted in 900.859 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -5408,10 +5408,10 @@ error </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.4 -R version used for fitting: 4.2.3 -Date of fit: Thu Apr 20 21:04:32 2023 -Date of summary: Thu Apr 20 21:04:34 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:13:37 2023 +Date of summary: Fri May 19 18:14:01 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5429,7 +5429,7 @@ Data: Model predictions using solution type deSolve -Fitted in 910.017 s +Fitted in 903.326 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5578,13 +5578,13 @@ JSE76 26.89 89.33 NA NA NA <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -5594,37 +5594,40 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 - [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 - [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 -[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 -[21] readxl_1.4.2 lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 -[25] gtable_0.3.3 cellranger_1.1.0 ragg_1.2.5 codetools_0.2-19 -[29] memoise_2.0.1 evaluate_0.20 inline_0.3.19 callr_3.7.3 -[33] fastmap_1.1.1 ps_1.7.4 lmtest_0.9-40 fansi_1.0.4 -[37] highr_0.10 scales_1.2.1 cachem_1.0.7 desc_1.4.2 -[41] jsonlite_1.8.4 systemfonts_1.0.4 fs_1.6.1 textshaping_0.3.6 -[45] gridExtra_2.3 ggplot2_3.4.2 digest_0.6.31 stringi_1.7.12 -[49] processx_3.8.0 dplyr_1.1.1 grid_4.2.3 rprojroot_2.0.3 -[53] cli_3.6.1 tools_4.2.3 magrittr_2.0.3 sass_0.4.5 -[57] tibble_3.2.1 crayon_1.5.2 pkgconfig_2.0.3 prettyunits_1.1.1 -[61] rmarkdown_2.21 R6_2.5.1 mclust_6.0.0 nlme_3.1-162 -[65] compiler_4.2.3 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.4 processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 +[17] DBI_1.1.3 mclust_6.0.0 ps_1.7.5 gridExtra_2.3 +[21] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 +[25] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 +[29] rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 +[33] inline_0.3.19 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 +[37] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 +[41] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 +[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 +[49] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[53] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[57] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[61] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1 +[65] readxl_1.4.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/dev/articles/prebuilt/2022_dmta_parent.html b/docs/dev/articles/prebuilt/2022_dmta_parent.html index 92259add..45a925b3 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_parent.html +++ b/docs/dev/articles/prebuilt/2022_dmta_parent.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ with residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 16 April 2023</h4> +2023, last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_parent.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_parent.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_parent.rmd</code></div> @@ -155,7 +155,7 @@ FOMC, DFOP and HS can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.3. It contains the test data +<p>The mkin package is used in version 1.2.5. It contains the test data and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot function available.</p> @@ -1287,10 +1287,10 @@ Plot of the final NLHM DFOP fit <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_tc_no_ranef_k2</span><span class="op">)</span></span></code></pre></div> <pre><code>saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:51 2023 -Date of summary: Sat Jan 28 11:22:52 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:27 2023 +Date of summary: Fri May 19 18:14:28 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1302,7 +1302,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.74 s +Fitted in 4.477 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1463,10 +1463,10 @@ Hierarchical mkin fit of the SFO model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:44 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:19 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1476,7 +1476,7 @@ Data: Model predictions using solution type analytical -Fitted in 0.982 s +Fitted in 1.091 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1535,10 +1535,10 @@ Hierarchical mkin fit of the SFO model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:21 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1548,7 +1548,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.39 s +Fitted in 2.517 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1609,10 +1609,10 @@ Hierarchical mkin fit of the FOMC model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1622,7 +1622,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.552 s +Fitted in 1.25 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1686,10 +1686,10 @@ Hierarchical mkin fit of the FOMC model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:21 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1699,7 +1699,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.764 s +Fitted in 2.666 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1765,10 +1765,10 @@ Hierarchical mkin fit of the DFOP model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1780,7 +1780,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.649 s +Fitted in 1.639 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1849,10 +1849,10 @@ Hierarchical mkin fit of the DFOP model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:22 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1864,7 +1864,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.288 s +Fitted in 3.435 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1935,10 +1935,10 @@ Hierarchical mkin fit of the HS model with error model const </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:45 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:20 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -1948,7 +1948,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.006 s +Fitted in 1.946 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -2017,10 +2017,10 @@ Hierarchical mkin fit of the HS model with error model tc </caption> <pre><code> saemix version used for fitting: 3.2 -mkin version used for pre-fitting: 1.2.2 -R version used for fitting: 4.2.2 -Date of fit: Sat Jan 28 11:22:46 2023 -Date of summary: Sat Jan 28 11:23:57 2023 +mkin version used for pre-fitting: 1.2.5 +R version used for fitting: 4.3.0 +Date of fit: Fri May 19 18:14:22 2023 +Date of summary: Fri May 19 18:15:34 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA @@ -2030,7 +2030,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.267 s +Fitted in 3.626 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -2144,13 +2144,13 @@ Convergence plot for the NLHM HS fit with two-component error <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.2 Patched (2022-11-10 r83330) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Debian GNU/Linux bookworm/sid +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -2160,35 +2160,37 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.41 mkin_1.2.2 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.34 zoo_1.8-11 tidyselect_1.2.0 xfun_0.35 - [5] bslib_0.4.2 purrr_1.0.0 lattice_0.20-45 colorspace_2.0-3 - [9] vctrs_0.5.1 generics_0.1.3 htmltools_0.5.4 yaml_2.3.6 -[13] utf8_1.2.2 rlang_1.0.6 pkgdown_2.0.7 jquerylib_0.1.4 -[17] pillar_1.8.1 glue_1.6.2 DBI_1.1.3 lifecycle_1.0.3 -[21] stringr_1.5.0 munsell_0.5.0 gtable_0.3.1 ragg_1.2.4 -[25] codetools_0.2-18 memoise_2.0.1 evaluate_0.19 fastmap_1.1.0 -[29] lmtest_0.9-40 fansi_1.0.3 highr_0.9 scales_1.2.1 -[33] cachem_1.0.6 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[37] fs_1.5.2 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.0 -[41] digest_0.6.31 stringi_1.7.8 dplyr_1.0.10 grid_4.2.2 -[45] rprojroot_2.0.3 cli_3.5.0 tools_4.2.2 magrittr_2.0.3 -[49] sass_0.4.4 tibble_3.1.8 pkgconfig_2.0.3 assertthat_0.2.1 -[53] rmarkdown_2.19 R6_2.5.1 mclust_6.0.0 nlme_3.1-161 -[57] compiler_4.2.2 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 memoise_2.0.1 +[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 +[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 +[37] fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 +[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[45] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[53] nlme_3.1-162 rmarkdown_2.21 compiler_4.3.0 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64940452 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/dev/articles/prebuilt/2022_dmta_pathway.html b/docs/dev/articles/prebuilt/2022_dmta_pathway.html index 959f3429..1861db06 100644 --- a/docs/dev/articles/prebuilt/2022_dmta_pathway.html +++ b/docs/dev/articles/prebuilt/2022_dmta_pathway.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ residue data on dimethenamid and dimethenamid-P</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 20 April 2023</h4> +last compiled on 19 Mai 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2022_dmta_pathway.rmd" class="external-link"><code>vignettes/prebuilt/2022_dmta_pathway.rmd</code></a></small> <div class="hidden name"><code>2022_dmta_pathway.rmd</code></div> @@ -156,7 +156,7 @@ can be fitted with the mkin package.</p> 173340 (Application of nonlinear hierarchical models to the kinetic evaluation of chemical degradation data) of the German Environment Agency carried out in 2022 and 2023.</p> -<p>The mkin package is used in version 1.2.4, which is currently under +<p>The mkin package is used in version 1.2.5, which is currently under development. It contains the test data, and the functions used in the evaluations. The <code>saemix</code> package is used as a backend for fitting the NLHM, but is also loaded to make the convergence plot @@ -1972,13 +1972,13 @@ error<a class="anchor" aria-label="anchor" href="#improved-fit-of-the-sforb-path <div class="section level3"> <h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h3> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -1988,36 +1988,39 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.4 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.5 loaded via a namespace (and not attached): - [1] deSolve_1.35 zoo_1.8-12 tidyselect_1.2.0 xfun_0.38 - [5] bslib_0.4.2 purrr_1.0.1 lattice_0.21-8 colorspace_2.1-0 - [9] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7 -[13] utf8_1.2.3 rlang_1.1.0 pkgbuild_1.4.0 pkgdown_2.0.7 -[17] jquerylib_0.1.4 pillar_1.9.0 glue_1.6.2 DBI_1.1.3 -[21] lifecycle_1.0.3 stringr_1.5.0 munsell_0.5.0 gtable_0.3.3 -[25] ragg_1.2.5 codetools_0.2-19 memoise_2.0.1 evaluate_0.20 -[29] inline_0.3.19 callr_3.7.3 fastmap_1.1.1 ps_1.7.4 -[33] lmtest_0.9-40 fansi_1.0.4 highr_0.10 scales_1.2.1 -[37] cachem_1.0.7 desc_1.4.2 jsonlite_1.8.4 systemfonts_1.0.4 -[41] fs_1.6.1 textshaping_0.3.6 gridExtra_2.3 ggplot2_3.4.2 -[45] digest_0.6.31 stringi_1.7.12 processx_3.8.0 dplyr_1.1.1 -[49] grid_4.2.3 rprojroot_2.0.3 cli_3.6.1 tools_4.2.3 -[53] magrittr_2.0.3 sass_0.4.5 tibble_3.2.1 crayon_1.5.2 -[57] pkgconfig_2.0.3 prettyunits_1.1.1 rmarkdown_2.21 R6_2.5.1 -[61] mclust_6.0.0 nlme_3.1-162 compiler_4.2.3 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] processx_3.8.1 pkgbuild_1.4.0 deSolve_1.35 DBI_1.1.3 +[17] mclust_6.0.0 ps_1.7.5 gridExtra_2.3 purrr_1.0.1 +[21] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[25] jquerylib_0.1.4 cli_3.6.1 crayon_1.5.2 rlang_1.1.1 +[29] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 inline_0.3.19 +[33] tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 +[37] ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 +[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 ragg_1.2.5 +[45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 +[49] bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 +[53] systemfonts_1.0.4 highr_0.10 xfun_0.39 tibble_3.2.1 +[57] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 +[61] rmarkdown_2.21 compiler_4.3.0 prettyunits_1.1.1</code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> </h3> <pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> -<pre><code>MemTotal: 64936316 kB</code></pre> +<pre><code>MemTotal: 64925476 kB</code></pre> </div> </div> </div> diff --git a/docs/dev/articles/prebuilt/2023_mesotrione_parent.html b/docs/dev/articles/prebuilt/2023_mesotrione_parent.html new file mode 100644 index 00000000..e3f2794f --- /dev/null +++ b/docs/dev/articles/prebuilt/2023_mesotrione_parent.html @@ -0,0 +1,2564 @@ +<!DOCTYPE html> +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"> +<head> +<meta http-equiv="Content-Type" content="text/html; 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class="page-header toc-ignore"> + <h1 data-toc-skip>Testing covariate modelling in hierarchical +parent degradation kinetics with residue data on mesotrione</h1> + <h4 data-toc-skip class="author">Johannes +Ranke</h4> + + <h4 data-toc-skip class="date">Last change on 4 August 2023, +last compiled on 10 August 2023</h4> + + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/prebuilt/2023_mesotrione_parent.rmd" class="external-link"><code>vignettes/prebuilt/2023_mesotrione_parent.rmd</code></a></small> + <div class="hidden name"><code>2023_mesotrione_parent.rmd</code></div> + + </div> + + + +<div class="section level2"> +<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a> +</h2> +<p>The purpose of this document is to test demonstrate how nonlinear +hierarchical models (NLHM) based on the parent degradation models SFO, +FOMC, DFOP and HS can be fitted with the mkin package, also considering +the influence of covariates like soil pH on different degradation +parameters. Because in some other case studies, the SFORB +parameterisation of biexponential decline has shown some advantages over +the DFOP parameterisation, SFORB was included in the list of tested +models as well.</p> +<p>The mkin package is used in version 1.2.6, which is contains the +functions that were used for the evaluations. The <code>saemix</code> +package is used as a backend for fitting the NLHM, but is also loaded to +make the convergence plot function available.</p> +<p>This document is processed with the <code>knitr</code> package, which +also provides the <code>kable</code> function that is used to improve +the display of tabular data in R markdown documents. For parallel +processing, the <code>parallel</code> package is used.</p> +<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/">mkin</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://yihui.org/knitr/" class="external-link">knitr</a></span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">saemix</span><span class="op">)</span></span> +<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va">parallel</span><span class="op">)</span></span> +<span><span class="va">n_cores</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span></span> +<span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="op">}</span> <span class="kw">else</span> <span class="op">{</span></span> +<span> <span class="va">cl</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeForkCluster</a></span><span class="op">(</span><span class="va">n_cores</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<div class="section level3"> +<h3 id="test-data">Test data<a class="anchor" aria-label="anchor" href="#test-data"></a> +</h3> +<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">data_file</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span></span> +<span> <span class="st">"testdata"</span>, <span class="st">"mesotrione_soil_efsa_2016.xlsx"</span>, package <span class="op">=</span> <span class="st">"mkin"</span><span class="op">)</span></span> +<span><span class="va">meso_ds</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/read_spreadsheet.html">read_spreadsheet</a></span><span class="op">(</span><span class="va">data_file</span>, parent_only <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<p>The following tables show the covariate data and the 18 datasets that +were read in from the spreadsheet file.</p> +<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">pH</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/attr.html" class="external-link">attr</a></span><span class="op">(</span><span class="va">meso_ds</span>, <span class="st">"covariates"</span><span class="op">)</span></span> +<span><span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="va">pH</span>, caption <span class="op">=</span> <span class="st">"Covariate data"</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<caption>Covariate data</caption> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">pH</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">Richmond</td> +<td align="right">6.2</td> +</tr> +<tr class="even"> +<td align="left">Richmond 2</td> +<td align="right">6.2</td> +</tr> +<tr class="odd"> +<td align="left">ERTC</td> +<td align="right">6.4</td> +</tr> +<tr class="even"> +<td align="left">Toulouse</td> +<td align="right">7.7</td> +</tr> +<tr class="odd"> +<td align="left">Picket Piece</td> +<td align="right">7.1</td> +</tr> +<tr class="even"> +<td align="left">721</td> +<td align="right">5.6</td> +</tr> +<tr class="odd"> +<td align="left">722</td> +<td align="right">5.7</td> +</tr> +<tr class="even"> +<td align="left">723</td> +<td align="right">5.4</td> +</tr> +<tr class="odd"> +<td align="left">724</td> +<td align="right">4.8</td> +</tr> +<tr class="even"> +<td align="left">725</td> +<td align="right">5.8</td> +</tr> +<tr class="odd"> +<td align="left">727</td> +<td align="right">5.1</td> +</tr> +<tr class="even"> +<td align="left">728</td> +<td align="right">5.9</td> +</tr> +<tr class="odd"> +<td align="left">729</td> +<td align="right">5.6</td> +</tr> +<tr class="even"> +<td align="left">730</td> +<td align="right">5.3</td> +</tr> +<tr class="odd"> +<td align="left">731</td> +<td align="right">6.1</td> +</tr> +<tr class="even"> +<td align="left">732</td> +<td align="right">5.0</td> +</tr> +<tr class="odd"> +<td align="left">741</td> +<td align="right">5.7</td> +</tr> +<tr class="even"> +<td align="left">742</td> +<td align="right">7.2</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="kw">for</span> <span class="op">(</span><span class="va">ds_name</span> <span class="kw">in</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">meso_ds</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span> +<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span></span> +<span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mkin_long_to_wide.html">mkin_long_to_wide</a></span><span class="op">(</span><span class="va">meso_ds</span><span class="op">[[</span><span class="va">ds_name</span><span class="op">]</span><span class="op">]</span><span class="op">)</span>,</span> +<span> caption <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="va">ds_name</span><span class="op">)</span>,</span> +<span> booktabs <span class="op">=</span> <span class="cn">TRUE</span>, row.names <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="op">}</span></span></code></pre></div> +<table class="table"> +<caption>Dataset Richmond</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">91.00</td> +</tr> +<tr class="even"> +<td align="right">1.179050</td> +<td align="right">86.70</td> +</tr> +<tr class="odd"> +<td align="right">3.537149</td> +<td align="right">73.60</td> +</tr> +<tr class="even"> +<td align="right">7.074299</td> +<td align="right">61.50</td> +</tr> +<tr class="odd"> +<td align="right">10.611448</td> +<td align="right">55.70</td> +</tr> +<tr class="even"> +<td align="right">15.327647</td> +<td align="right">47.70</td> +</tr> +<tr class="odd"> +<td align="right">17.685747</td> +<td align="right">39.50</td> +</tr> +<tr class="even"> +<td align="right">24.760046</td> +<td align="right">29.80</td> +</tr> +<tr class="odd"> +<td align="right">35.371494</td> +<td align="right">19.60</td> +</tr> +<tr class="even"> +<td align="right">68.384889</td> +<td align="right">5.67</td> +</tr> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">97.90</td> +</tr> +<tr class="even"> +<td align="right">1.179050</td> +<td align="right">96.40</td> +</tr> +<tr class="odd"> +<td align="right">3.537149</td> +<td align="right">89.10</td> +</tr> +<tr class="even"> +<td align="right">7.074299</td> +<td align="right">74.40</td> +</tr> +<tr class="odd"> +<td align="right">10.611448</td> +<td align="right">57.40</td> +</tr> +<tr class="even"> +<td align="right">15.327647</td> +<td align="right">46.30</td> +</tr> +<tr class="odd"> +<td align="right">18.864797</td> +<td align="right">35.50</td> +</tr> +<tr class="even"> +<td align="right">27.118146</td> +<td align="right">27.20</td> +</tr> +<tr class="odd"> +<td align="right">35.371494</td> +<td align="right">19.10</td> +</tr> +<tr class="even"> +<td align="right">74.280138</td> +<td align="right">6.50</td> +</tr> +<tr class="odd"> +<td align="right">108.472582</td> +<td align="right">3.40</td> +</tr> +<tr class="even"> +<td align="right">142.665027</td> +<td align="right">2.20</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Richmond 2</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">96.0</td> +</tr> +<tr class="even"> +<td align="right">2.422004</td> +<td align="right">82.4</td> +</tr> +<tr class="odd"> +<td align="right">5.651343</td> +<td align="right">71.2</td> +</tr> +<tr class="even"> +<td align="right">8.073348</td> +<td align="right">53.1</td> +</tr> +<tr class="odd"> +<td align="right">11.302687</td> +<td align="right">48.5</td> +</tr> +<tr class="even"> +<td align="right">16.954030</td> +<td align="right">33.4</td> +</tr> +<tr class="odd"> +<td align="right">22.605373</td> +<td align="right">24.2</td> +</tr> +<tr class="even"> +<td align="right">45.210746</td> +<td align="right">11.9</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset ERTC</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">99.9</td> +</tr> +<tr class="even"> +<td align="right">2.755193</td> +<td align="right">80.0</td> +</tr> +<tr class="odd"> +<td align="right">6.428782</td> +<td align="right">42.1</td> +</tr> +<tr class="even"> +<td align="right">9.183975</td> +<td align="right">50.1</td> +</tr> +<tr class="odd"> +<td align="right">12.857565</td> +<td align="right">28.4</td> +</tr> +<tr class="even"> +<td align="right">19.286347</td> +<td align="right">39.8</td> +</tr> +<tr class="odd"> +<td align="right">25.715130</td> +<td align="right">29.9</td> +</tr> +<tr class="even"> +<td align="right">51.430259</td> +<td align="right">2.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Toulouse</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">96.8</td> +</tr> +<tr class="even"> +<td align="right">2.897983</td> +<td align="right">63.3</td> +</tr> +<tr class="odd"> +<td align="right">6.761960</td> +<td align="right">22.3</td> +</tr> +<tr class="even"> +<td align="right">9.659942</td> +<td align="right">16.6</td> +</tr> +<tr class="odd"> +<td align="right">13.523919</td> +<td align="right">16.1</td> +</tr> +<tr class="even"> +<td align="right">20.285879</td> +<td align="right">17.2</td> +</tr> +<tr class="odd"> +<td align="right">27.047838</td> +<td align="right">1.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset Picket Piece</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">102.0</td> +</tr> +<tr class="even"> +<td align="right">2.841195</td> +<td align="right">73.7</td> +</tr> +<tr class="odd"> +<td align="right">6.629454</td> +<td align="right">35.5</td> +</tr> +<tr class="even"> +<td align="right">9.470649</td> +<td align="right">31.8</td> +</tr> +<tr class="odd"> +<td align="right">13.258909</td> +<td align="right">18.0</td> +</tr> +<tr class="even"> +<td align="right">19.888364</td> +<td align="right">3.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 721</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">86.4</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">61.4</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">49.8</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">41.0</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">35.1</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 722</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">52.1</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">37.4</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">21.2</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">14.3</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 723</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">89.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">70.8</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">51.1</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">42.7</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">26.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 724</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.000000</td> +<td align="right">89.4</td> +</tr> +<tr class="even"> +<td align="right">9.008208</td> +<td align="right">65.2</td> +</tr> +<tr class="odd"> +<td align="right">18.016415</td> +<td align="right">55.8</td> +</tr> +<tr class="even"> +<td align="right">27.024623</td> +<td align="right">46.0</td> +</tr> +<tr class="odd"> +<td align="right">36.032831</td> +<td align="right">41.7</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 725</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">89.0</td> +</tr> +<tr class="even"> +<td align="right">10.99058</td> +<td align="right">35.4</td> +</tr> +<tr class="odd"> +<td align="right">21.98116</td> +<td align="right">18.6</td> +</tr> +<tr class="even"> +<td align="right">32.97174</td> +<td align="right">11.6</td> +</tr> +<tr class="odd"> +<td align="right">43.96232</td> +<td align="right">7.6</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 727</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.3</td> +</tr> +<tr class="even"> +<td align="right">10.96104</td> +<td align="right">63.2</td> +</tr> +<tr class="odd"> +<td align="right">21.92209</td> +<td align="right">51.1</td> +</tr> +<tr class="even"> +<td align="right">32.88313</td> +<td align="right">42.0</td> +</tr> +<tr class="odd"> +<td align="right">43.84417</td> +<td align="right">40.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 728</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.8</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">43.6</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">22.0</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">15.9</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">8.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 729</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">91.6</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">60.5</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">43.5</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">28.4</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">20.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 730</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.7</td> +</tr> +<tr class="even"> +<td align="right">11.07446</td> +<td align="right">58.9</td> +</tr> +<tr class="odd"> +<td align="right">22.14893</td> +<td align="right">44.0</td> +</tr> +<tr class="even"> +<td align="right">33.22339</td> +<td align="right">46.0</td> +</tr> +<tr class="odd"> +<td align="right">44.29785</td> +<td align="right">29.3</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 731</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.1</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">64.4</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">45.3</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">33.6</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">23.5</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 732</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">58.2</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">40.1</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">33.1</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">25.8</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 741</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">90.3</td> +</tr> +<tr class="even"> +<td align="right">10.84712</td> +<td align="right">68.7</td> +</tr> +<tr class="odd"> +<td align="right">21.69424</td> +<td align="right">58.0</td> +</tr> +<tr class="even"> +<td align="right">32.54136</td> +<td align="right">52.2</td> +</tr> +<tr class="odd"> +<td align="right">43.38848</td> +<td align="right">48.0</td> +</tr> +</tbody> +</table> +<table class="table"> +<caption>Dataset 742</caption> +<thead><tr class="header"> +<th align="right">time</th> +<th align="right">meso</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="right">0.00000</td> +<td align="right">92.0</td> +</tr> +<tr class="even"> +<td align="right">11.24366</td> +<td align="right">60.9</td> +</tr> +<tr class="odd"> +<td align="right">22.48733</td> +<td align="right">36.2</td> +</tr> +<tr class="even"> +<td align="right">33.73099</td> +<td align="right">18.3</td> +</tr> +<tr class="odd"> +<td align="right">44.97466</td> +<td align="right">8.7</td> +</tr> +</tbody> +</table> +</div> +</div> +<div class="section level2"> +<h2 id="separate-evaluations">Separate evaluations<a class="anchor" aria-label="anchor" href="#separate-evaluations"></a> +</h2> +<p>In order to obtain suitable starting parameters for the NLHM fits, +separate fits of the five models to the data for each soil are generated +using the <code>mmkin</code> function from the mkin package. In a first +step, constant variance is assumed. Convergence is checked with the +<code>status</code> function.</p> +<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">deg_mods</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>, <span class="st">"SFORB"</span>, <span class="st">"HS"</span><span class="op">)</span></span> +<span><span class="va">f_sep_const</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mmkin.html">mmkin</a></span><span class="op">(</span></span> +<span> <span class="va">deg_mods</span>,</span> +<span> <span class="va">meso_ds</span>,</span> +<span> error_model <span class="op">=</span> <span class="st">"const"</span>,</span> +<span> cluster <span class="op">=</span> <span class="va">cl</span>,</span> +<span> quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">Richmond</th> +<th align="left">Richmond 2</th> +<th align="left">ERTC</th> +<th align="left">Toulouse</th> +<th align="left">Picket Piece</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">18</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="10%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">721</th> +<th align="left">722</th> +<th align="left">723</th> +<th align="left">724</th> +<th align="left">725</th> +<th align="left">727</th> +<th align="left">728</th> +<th align="left">729</th> +<th align="left">730</th> +<th align="left">731</th> +<th align="left">732</th> +<th align="left">741</th> +<th align="left">742</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>In the tables above, OK indicates convergence and C indicates failure +to converge. Most separate fits with constant variance converged, with +the exception of two FOMC fits, one SFORB fit and one HS fit.</p> +<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_sep_tc</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_sep_const</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_tc</span><span class="op">[</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">Richmond</th> +<th align="left">Richmond 2</th> +<th align="left">ERTC</th> +<th align="left">Toulouse</th> +<th align="left">Picket Piece</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_sep_tc</span><span class="op">[</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">18</span><span class="op">]</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="10%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +<col width="6%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">721</th> +<th align="left">722</th> +<th align="left">723</th> +<th align="left">724</th> +<th align="left">725</th> +<th align="left">727</th> +<th align="left">728</th> +<th align="left">729</th> +<th align="left">730</th> +<th align="left">731</th> +<th align="left">732</th> +<th align="left">741</th> +<th align="left">742</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">C</td> +<td align="left">OK</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>With the two-component error model, the set of fits that did not +converge is larger, with convergence problems appearing for a number of +non-SFO fits.</p> +</div> +<div class="section level2"> +<h2 id="hierarchical-model-fits-without-covariate-effect">Hierarchical model fits without covariate effect<a class="anchor" aria-label="anchor" href="#hierarchical-model-fits-without-covariate-effect"></a> +</h2> +<p>The following code fits hierarchical kinetic models for the ten +combinations of the five different degradation models with the two +different error models in parallel.</p> +<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_1</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/mhmkin.html">mhmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">f_sep_const</span>, <span class="va">f_sep_tc</span><span class="op">)</span>, cluster <span class="op">=</span> <span class="va">cl</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>All fits terminate without errors (status OK).</p> +<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">npar</th> +<th align="right">AIC</th> +<th align="right">BIC</th> +<th align="right">Lik</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO const</td> +<td align="right">5</td> +<td align="right">800.0</td> +<td align="right">804.5</td> +<td align="right">-395.0</td> +</tr> +<tr class="even"> +<td align="left">SFO tc</td> +<td align="right">6</td> +<td align="right">801.9</td> +<td align="right">807.2</td> +<td align="right">-394.9</td> +</tr> +<tr class="odd"> +<td align="left">FOMC const</td> +<td align="right">7</td> +<td align="right">787.4</td> +<td align="right">793.6</td> +<td align="right">-386.7</td> +</tr> +<tr class="even"> +<td align="left">FOMC tc</td> +<td align="right">8</td> +<td align="right">788.9</td> +<td align="right">796.1</td> +<td align="right">-386.5</td> +</tr> +<tr class="odd"> +<td align="left">DFOP const</td> +<td align="right">9</td> +<td align="right">787.6</td> +<td align="right">795.6</td> +<td align="right">-384.8</td> +</tr> +<tr class="even"> +<td align="left">SFORB const</td> +<td align="right">9</td> +<td align="right">787.4</td> +<td align="right">795.4</td> +<td align="right">-384.7</td> +</tr> +<tr class="odd"> +<td align="left">HS const</td> +<td align="right">9</td> +<td align="right">781.9</td> +<td align="right">789.9</td> +<td align="right">-382.0</td> +</tr> +<tr class="even"> +<td align="left">DFOP tc</td> +<td align="right">10</td> +<td align="right">787.4</td> +<td align="right">796.3</td> +<td align="right">-383.7</td> +</tr> +<tr class="odd"> +<td align="left">SFORB tc</td> +<td align="right">10</td> +<td align="right">795.8</td> +<td align="right">804.7</td> +<td align="right">-387.9</td> +</tr> +<tr class="even"> +<td align="left">HS tc</td> +<td align="right">10</td> +<td align="right">783.7</td> +<td align="right">792.7</td> +<td align="right">-381.9</td> +</tr> +</tbody> +</table> +<p>The model comparisons show that the fits with constant variance are +consistently preferable to the corresponding fits with two-component +error for these data. This is confirmed by the fact that the parameter +<code>b.1</code> (the relative standard deviation in the fits obtained +with the saemix package), is ill-defined in all fits.</p> +<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<colgroup> +<col width="6%"> +<col width="44%"> +<col width="49%"> +</colgroup> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">sd(meso_0)</td> +<td align="left">sd(meso_0), b.1</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">sd(meso_0), sd(log_beta)</td> +<td align="left">sd(meso_0), sd(log_beta), b.1</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">sd(meso_0), sd(log_k1)</td> +<td align="left">sd(meso_0), sd(g_qlogis), b.1</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">sd(meso_free_0), sd(log_k_meso_free_bound)</td> +<td align="left">sd(meso_free_0), sd(log_k_meso_free_bound), b.1</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">sd(meso_0)</td> +<td align="left">sd(meso_0), b.1</td> +</tr> +</tbody> +</table> +<p>For obtaining fits with only well-defined random effects, we update +the set of fits, excluding random effects that were ill-defined +according to the <code>illparms</code> function.</p> +<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">f_saem_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">f_saem_1</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_1</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/status.html">status</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left">OK</td> +<td align="left">OK</td> +</tr> +</tbody> +</table> +<p>The updated fits terminate without errors.</p> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">)</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="left">const</th> +<th align="left">tc</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">SFO</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="even"> +<td align="left">FOMC</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="odd"> +<td align="left">DFOP</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="even"> +<td align="left">SFORB</td> +<td align="left"></td> +<td align="left">b.1</td> +</tr> +<tr class="odd"> +<td align="left">HS</td> +<td align="left"></td> +<td align="left"></td> +</tr> +</tbody> +</table> +<p>No ill-defined errors remain in the fits with constant variance.</p> +</div> +<div class="section level2"> +<h2 id="hierarchical-model-fits-with-covariate-effect">Hierarchical model fits with covariate effect<a class="anchor" aria-label="anchor" href="#hierarchical-model-fits-with-covariate-effect"></a> +</h2> +<p>In the following sections, hierarchical fits including a model for +the influence of pH on selected degradation parameters are shown for all +parent models. Constant variance is selected as the error model based on +the fits without covariate effects. Random effects that were ill-defined +in the fits without pH influence are excluded. A potential influence of +the soil pH is only included for parameters with a well-defined random +effect, because experience has shown that only for such parameters a +significant pH effect could be found.</p> +<div class="section level3"> +<h3 id="sfo">SFO<a class="anchor" aria-label="anchor" href="#sfo"></a> +</h3> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sfo_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="st">"meso_0"</span>, covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">sfo_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">91.35</td> +<td align="right">89.27</td> +<td align="right">93.43</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso</td> +<td align="right">-6.66</td> +<td align="right">-7.97</td> +<td align="right">-5.35</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso)</td> +<td align="right">0.59</td> +<td align="right">0.37</td> +<td align="right">0.81</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">5.48</td> +<td align="right">4.71</td> +<td align="right">6.24</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso</td> +<td align="right">0.35</td> +<td align="right">0.23</td> +<td align="right">0.47</td> +</tr> +</tbody> +</table> +<p>The parameter showing the pH influence in the above table is +<code>beta_pH(log_k_meso)</code>. Its confidence interval does not +include zero, indicating that the influence of soil pH on the log of the +degradation rate constant is significantly greater than zero.</p> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"SFO"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">sfo_pH</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["SFO", "const"]] 4 797.56 801.12 -394.78 +sfo_pH 5 783.09 787.54 -386.54 16.473 1 4.934e-05 *** +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>The comparison with the SFO fit without covariate effect confirms +that considering the soil pH improves the model, both by comparison of +AIC and BIC and by the likelihood ratio test.</p> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sfo_pH</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-8-1.png" width="700" style="display: block; margin: auto;"></p> +<p>Endpoints for a model with covariates are by default calculated for +the median of the covariate values. This quantile can be adapted, or a +specific covariate value can be given as shown below.</p> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 +meso 18.52069 61.52441</code></pre> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span>, covariate_quantile <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +90% 7.13 + +$distimes + DT50 DT90 +meso 8.237019 27.36278</code></pre> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sfo_pH</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7.0</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 +meso 8.89035 29.5331</code></pre> +</div> +<div class="section level3"> +<h3 id="fomc">FOMC<a class="anchor" aria-label="anchor" href="#fomc"></a> +</h3> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">fomc_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="st">"meso_0"</span>, covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_alpha</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fomc_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">92.84</td> +<td align="right">90.75</td> +<td align="right">94.93</td> +</tr> +<tr class="even"> +<td align="left">log_alpha</td> +<td align="right">-2.21</td> +<td align="right">-3.49</td> +<td align="right">-0.92</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_alpha)</td> +<td align="right">0.58</td> +<td align="right">0.37</td> +<td align="right">0.79</td> +</tr> +<tr class="even"> +<td align="left">log_beta</td> +<td align="right">4.21</td> +<td align="right">3.44</td> +<td align="right">4.99</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">5.03</td> +<td align="right">4.32</td> +<td align="right">5.73</td> +</tr> +<tr class="even"> +<td align="left">SD.log_alpha</td> +<td align="right">0.00</td> +<td align="right">-23.77</td> +<td align="right">23.78</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_beta</td> +<td align="right">0.37</td> +<td align="right">0.01</td> +<td align="right">0.74</td> +</tr> +</tbody> +</table> +<p>As in the case of SFO, the confidence interval of the slope parameter +(here <code>beta_pH(log_alpha)</code>) quantifying the influence of soil +pH does not include zero, and the model comparison clearly indicates +that the model with covariate influence is preferable. However, the +random effect for <code>alpha</code> is not well-defined any more after +inclusion of the covariate effect (the confidence interval of +<code>SD.log_alpha</code> includes zero).</p> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">fomc_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_alpha)"</code></pre> +<p>Therefore, the model is updated without this random effect, and no +ill-defined parameters remain.</p> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">fomc_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">fomc_pH</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_alpha"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"FOMC"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">fomc_pH</span>, <span class="va">fomc_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["FOMC", "const"]] 5 783.25 787.71 -386.63 +fomc_pH_2 6 767.49 772.83 -377.75 17.762 1 2.503e-05 *** +fomc_pH 7 770.07 776.30 -378.04 0.000 1 1 +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>Model comparison indicates that including pH dependence significantly +improves the fit, and that the reduced model with covariate influence +results in the most preferable FOMC fit.</p> +<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.05</td> +<td align="right">90.98</td> +<td align="right">95.13</td> +</tr> +<tr class="even"> +<td align="left">log_alpha</td> +<td align="right">-2.91</td> +<td align="right">-4.18</td> +<td align="right">-1.63</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_alpha)</td> +<td align="right">0.66</td> +<td align="right">0.44</td> +<td align="right">0.87</td> +</tr> +<tr class="even"> +<td align="left">log_beta</td> +<td align="right">3.95</td> +<td align="right">3.29</td> +<td align="right">4.62</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.98</td> +<td align="right">4.28</td> +<td align="right">5.68</td> +</tr> +<tr class="even"> +<td align="left">SD.log_beta</td> +<td align="right">0.40</td> +<td align="right">0.26</td> +<td align="right">0.54</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-14-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fomc_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back +meso 17.30248 82.91343 24.95943</code></pre> +<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fomc_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back +meso 6.986239 27.02927 8.136621</code></pre> +</div> +<div class="section level3"> +<h3 id="dfop">DFOP<a class="anchor" aria-label="anchor" href="#dfop"></a> +</h3> +<p>In the DFOP fits without covariate effects, random effects for two +degradation parameters (<code>k2</code> and <code>g</code>) were +identifiable.</p> +<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.61</td> +<td align="right">91.58</td> +<td align="right">95.63</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-1.53</td> +<td align="right">-2.27</td> +<td align="right">-0.79</td> +</tr> +<tr class="odd"> +<td align="left">log_k2</td> +<td align="right">-3.42</td> +<td align="right">-3.73</td> +<td align="right">-3.11</td> +</tr> +<tr class="even"> +<td align="left">g_qlogis</td> +<td align="right">-1.67</td> +<td align="right">-2.57</td> +<td align="right">-0.77</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.74</td> +<td align="right">4.02</td> +<td align="right">5.45</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.60</td> +<td align="right">0.38</td> +<td align="right">0.81</td> +</tr> +<tr class="odd"> +<td align="left">SD.g_qlogis</td> +<td align="right">0.94</td> +<td align="right">0.33</td> +<td align="right">1.54</td> +</tr> +</tbody> +</table> +<p>A fit with pH dependent degradation parameters was obtained by +excluding the same random effects as in the refined DFOP fit without +covariate influence, and including covariate models for the two +identifiable parameters <code>k2</code> and <code>g</code>.</p> +<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">g_qlogis</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<p>The corresponding parameters for the influence of soil pH are +<code>beta_pH(log_k2)</code> for the influence of soil pH on +<code>k2</code>, and <code>beta_pH(g_qlogis)</code> for its influence on +<code>g</code>.</p> +<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">dfop_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">92.84</td> +<td align="right">90.85</td> +<td align="right">94.84</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-2.82</td> +<td align="right">-3.09</td> +<td align="right">-2.54</td> +</tr> +<tr class="odd"> +<td align="left">log_k2</td> +<td align="right">-11.48</td> +<td align="right">-15.32</td> +<td align="right">-7.64</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">1.31</td> +<td align="right">0.69</td> +<td align="right">1.92</td> +</tr> +<tr class="odd"> +<td align="left">g_qlogis</td> +<td align="right">3.13</td> +<td align="right">0.47</td> +<td align="right">5.80</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(g_qlogis)</td> +<td align="right">-0.57</td> +<td align="right">-1.04</td> +<td align="right">-0.09</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.96</td> +<td align="right">4.26</td> +<td align="right">5.65</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.76</td> +<td align="right">0.47</td> +<td align="right">1.05</td> +</tr> +<tr class="odd"> +<td align="left">SD.g_qlogis</td> +<td align="right">0.01</td> +<td align="right">-9.96</td> +<td align="right">9.97</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(g_qlogis)"</code></pre> +<p>Confidence intervals for neither of them include zero, indicating a +significant difference from zero. However, the random effect for +<code>g</code> is now ill-defined. The fit is updated without this +ill-defined random effect.</p> +<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_pH</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span>, <span class="st">"g_qlogis"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "beta_pH(g_qlogis)"</code></pre> +<p>Now, the slope parameter for the pH effect on <code>g</code> is +ill-defined. Therefore, another attempt is made without the +corresponding covariate model.</p> +<div class="sourceCode" id="cb47"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_3</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_3</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(g_qlogis)"</code></pre> +<p>As the random effect for <code>g</code> is again ill-defined, the fit +is repeated without it.</p> +<div class="sourceCode" id="cb49"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">dfop_pH_4</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">dfop_pH_3</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span>, <span class="st">"log_k1"</span>, <span class="st">"g_qlogis"</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">dfop_pH_4</span><span class="op">)</span></span></code></pre></div> +<p>While no ill-defined parameters remain, model comparison suggests +that the previous model <code>dfop_pH_2</code> with two pH dependent +parameters is preferable, based on information criteria as well as based +on the likelihood ratio test.</p> +<div class="sourceCode" id="cb50"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"DFOP"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">dfop_pH</span>, <span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_3</span>, <span class="va">dfop_pH_4</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik +f_saem_2[["DFOP", "const"]] 7 782.94 789.18 -384.47 +dfop_pH_4 7 767.35 773.58 -376.68 +dfop_pH_2 8 765.14 772.26 -374.57 +dfop_pH_3 8 769.00 776.12 -376.50 +dfop_pH 9 769.10 777.11 -375.55</code></pre> +<div class="sourceCode" id="cb52"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_4</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +dfop_pH_4 7 767.35 773.58 -376.68 +dfop_pH_2 8 765.14 772.26 -374.57 4.2153 1 0.04006 * +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>When focussing on parameter identifiability using the test if the +confidence interval includes zero, <code>dfop_pH_4</code> would still be +the preferred model. However, it should be kept in mind that parameter +confidence intervals are constructed using a simple linearisation of the +likelihood. As the confidence interval of the random effect for +<code>g</code> only marginally includes zero, it is suggested that this +is acceptable, and that <code>dfop_pH_2</code> can be considered the +most preferable model.</p> +<div class="sourceCode" id="cb54"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-19-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb55"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 18.36876 73.51841 22.13125 4.191901 23.98672</code></pre> +<div class="sourceCode" id="cb57"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.346428 28.34437 8.532507 4.191901 8.753618</code></pre> +</div> +<div class="section level3"> +<h3 id="sforb">SFORB<a class="anchor" aria-label="anchor" href="#sforb"></a> +</h3> +<div class="sourceCode" id="cb59"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sforb_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"SFORB"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_free_0"</span>, <span class="st">"log_k_meso_free_bound"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso_free</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k_meso_bound_free</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb60"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">sforb_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_free_0</td> +<td align="right">93.42</td> +<td align="right">91.32</td> +<td align="right">95.52</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free</td> +<td align="right">-5.37</td> +<td align="right">-6.94</td> +<td align="right">-3.81</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso_free)</td> +<td align="right">0.42</td> +<td align="right">0.18</td> +<td align="right">0.67</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free_bound</td> +<td align="right">-3.49</td> +<td align="right">-4.92</td> +<td align="right">-2.05</td> +</tr> +<tr class="odd"> +<td align="left">log_k_meso_bound_free</td> +<td align="right">-9.98</td> +<td align="right">-19.22</td> +<td align="right">-0.74</td> +</tr> +<tr class="even"> +<td align="left">beta_pH(log_k_meso_bound_free)</td> +<td align="right">1.23</td> +<td align="right">-0.21</td> +<td align="right">2.67</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.90</td> +<td align="right">4.18</td> +<td align="right">5.63</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k_meso_free</td> +<td align="right">0.35</td> +<td align="right">0.23</td> +<td align="right">0.47</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso_bound_free</td> +<td align="right">0.13</td> +<td align="right">-1.95</td> +<td align="right">2.20</td> +</tr> +</tbody> +</table> +<p>The confidence interval of +<code>beta_pH(log_k_meso_bound_free)</code> includes zero, indicating +that the influence of soil pH on <code>k_meso_bound_free</code> cannot +reliably be quantified. Also, the confidence interval for the random +effect on this parameter (<code>SD.log_k_meso_bound_free</code>) +includes zero.</p> +<p>Using the <code>illparms</code> function, these ill-defined +parameters can be found more conveniently.</p> +<div class="sourceCode" id="cb61"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_k_meso_bound_free)" "beta_pH(log_k_meso_bound_free)"</code></pre> +<p>To remove the ill-defined parameters, a second variant of the SFORB +model with pH influence is fitted. No ill-defined parameters remain.</p> +<div class="sourceCode" id="cb63"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">sforb_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">sforb_pH</span>,</span> +<span> no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_free_0"</span>, <span class="st">"log_k_meso_free_bound"</span>, <span class="st">"log_k_meso_bound_free"</span><span class="op">)</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k_meso_free</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<p>The model comparison of the SFORB fits includes the refined model +without covariate effect, and both versions of the SFORB fit with +covariate effect.</p> +<div class="sourceCode" id="cb64"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"SFORB"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">sforb_pH</span>, <span class="va">sforb_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["SFORB", "const"]] 7 783.40 789.63 -384.70 +sforb_pH_2 7 770.94 777.17 -378.47 12.4616 0 +sforb_pH 9 768.81 776.83 -375.41 6.1258 2 0.04675 * +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<p>The first model including pH influence is preferable based on +information criteria and the likelihood ratio test. However, as it is +not fully identifiable, the second model is selected.</p> +<div class="sourceCode" id="cb66"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_free_0</td> +<td align="right">93.32</td> +<td align="right">91.16</td> +<td align="right">95.48</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free</td> +<td align="right">-6.15</td> +<td align="right">-7.43</td> +<td align="right">-4.86</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k_meso_free)</td> +<td align="right">0.54</td> +<td align="right">0.33</td> +<td align="right">0.75</td> +</tr> +<tr class="even"> +<td align="left">log_k_meso_free_bound</td> +<td align="right">-3.80</td> +<td align="right">-5.20</td> +<td align="right">-2.40</td> +</tr> +<tr class="odd"> +<td align="left">log_k_meso_bound_free</td> +<td align="right">-2.95</td> +<td align="right">-4.26</td> +<td align="right">-1.64</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">5.08</td> +<td align="right">4.38</td> +<td align="right">5.79</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k_meso_free</td> +<td align="right">0.33</td> +<td align="right">0.22</td> +<td align="right">0.45</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb67"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-25-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb68"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sforb_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$ff +meso_free + 1 + +$SFORB + meso_b1 meso_b2 meso_g +0.09735824 0.02631699 0.31602120 + +$distimes + DT50 DT90 DT50back DT50_meso_b1 DT50_meso_b2 +meso 16.86549 73.15824 22.02282 7.119554 26.33839</code></pre> +<div class="sourceCode" id="cb70"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">sforb_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$ff +meso_free + 1 + +$SFORB + meso_b1 meso_b2 meso_g +0.13315233 0.03795988 0.61186191 + +$distimes + DT50 DT90 DT50back DT50_meso_b1 DT50_meso_b2 +meso 7.932495 36.93311 11.11797 5.205671 18.26</code></pre> +</div> +<div class="section level3"> +<h3 id="hs">HS<a class="anchor" aria-label="anchor" href="#hs"></a> +</h3> +<div class="sourceCode" id="cb72"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">hs_pH</span> <span class="op"><-</span> <span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_sep_const</span><span class="op">[</span><span class="st">"HS"</span>, <span class="op">]</span>, no_random_effect <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"meso_0"</span><span class="op">)</span>,</span> +<span> covariates <span class="op">=</span> <span class="va">pH</span>,</span> +<span> covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k1</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_tb</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<div class="sourceCode" id="cb73"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">hs_pH</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.33</td> +<td align="right">91.47</td> +<td align="right">95.19</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-5.81</td> +<td align="right">-7.27</td> +<td align="right">-4.36</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k1)</td> +<td align="right">0.47</td> +<td align="right">0.23</td> +<td align="right">0.72</td> +</tr> +<tr class="even"> +<td align="left">log_k2</td> +<td align="right">-6.80</td> +<td align="right">-8.76</td> +<td align="right">-4.83</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">0.54</td> +<td align="right">0.21</td> +<td align="right">0.87</td> +</tr> +<tr class="even"> +<td align="left">log_tb</td> +<td align="right">3.25</td> +<td align="right">1.25</td> +<td align="right">5.25</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_tb)</td> +<td align="right">-0.10</td> +<td align="right">-0.43</td> +<td align="right">0.23</td> +</tr> +<tr class="even"> +<td align="left">a.1</td> +<td align="right">4.49</td> +<td align="right">3.78</td> +<td align="right">5.21</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k1</td> +<td align="right">0.37</td> +<td align="right">0.24</td> +<td align="right">0.51</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k2</td> +<td align="right">0.29</td> +<td align="right">0.10</td> +<td align="right">0.48</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_tb</td> +<td align="right">0.25</td> +<td align="right">-0.07</td> +<td align="right">0.57</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb74"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">hs_pH</span><span class="op">)</span></span></code></pre></div> +<pre><code>[1] "sd(log_tb)" "beta_pH(log_tb)"</code></pre> +<p>According to the output of the <code>illparms</code> function, the +random effect on the break time <code>tb</code> cannot reliably be +quantified, neither can the influence of soil pH on <code>tb</code>. The +fit is repeated without the corresponding covariate model, and no +ill-defined parameters remain.</p> +<div class="sourceCode" id="cb76"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="va">hs_pH_2</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">hs_pH</span>, covariate_models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">log_k1</span> <span class="op">~</span> <span class="va">pH</span>, <span class="va">log_k2</span> <span class="op">~</span> <span class="va">pH</span><span class="op">)</span><span class="op">)</span></span> +<span><span class="fu"><a href="../../reference/illparms.html">illparms</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<p>Model comparison confirms that this model is preferable to the fit +without covariate influence, and also to the first version with +covariate influence.</p> +<div class="sourceCode" id="cb77"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_saem_2</span><span class="op">[[</span><span class="st">"HS"</span>, <span class="st">"const"</span><span class="op">]</span><span class="op">]</span>, <span class="va">hs_pH</span>, <span class="va">hs_pH_2</span>, test <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik Chisq Df Pr(>Chisq) +f_saem_2[["HS", "const"]] 8 780.08 787.20 -382.04 +hs_pH_2 10 766.47 775.37 -373.23 17.606 2 0.0001503 *** +hs_pH 11 769.80 779.59 -373.90 0.000 1 1.0000000 +--- +Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1</code></pre> +<div class="sourceCode" id="cb79"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span><span class="op">$</span><span class="va">confint_trans</span> <span class="op">|></span> <span class="fu"><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">kable</a></span><span class="op">(</span>digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div> +<table class="table"> +<thead><tr class="header"> +<th align="left"></th> +<th align="right">est.</th> +<th align="right">lower</th> +<th align="right">upper</th> +</tr></thead> +<tbody> +<tr class="odd"> +<td align="left">meso_0</td> +<td align="right">93.33</td> +<td align="right">91.50</td> +<td align="right">95.15</td> +</tr> +<tr class="even"> +<td align="left">log_k1</td> +<td align="right">-5.68</td> +<td align="right">-7.09</td> +<td align="right">-4.27</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k1)</td> +<td align="right">0.46</td> +<td align="right">0.22</td> +<td align="right">0.69</td> +</tr> +<tr class="even"> +<td align="left">log_k2</td> +<td align="right">-6.61</td> +<td align="right">-8.34</td> +<td align="right">-4.88</td> +</tr> +<tr class="odd"> +<td align="left">beta_pH(log_k2)</td> +<td align="right">0.50</td> +<td align="right">0.21</td> +<td align="right">0.79</td> +</tr> +<tr class="even"> +<td align="left">log_tb</td> +<td align="right">2.70</td> +<td align="right">2.33</td> +<td align="right">3.08</td> +</tr> +<tr class="odd"> +<td align="left">a.1</td> +<td align="right">4.45</td> +<td align="right">3.74</td> +<td align="right">5.16</td> +</tr> +<tr class="even"> +<td align="left">SD.log_k1</td> +<td align="right">0.36</td> +<td align="right">0.22</td> +<td align="right">0.49</td> +</tr> +<tr class="odd"> +<td align="left">SD.log_k2</td> +<td align="right">0.23</td> +<td align="right">0.02</td> +<td align="right">0.43</td> +</tr> +<tr class="even"> +<td align="left">SD.log_tb</td> +<td align="right">0.55</td> +<td align="right">0.25</td> +<td align="right">0.85</td> +</tr> +</tbody> +</table> +<div class="sourceCode" id="cb80"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<p><img src="2023_mesotrione_parent_files/figure-html/unnamed-chunk-30-1.png" width="700" style="display: block; margin: auto;"></p> +<div class="sourceCode" id="cb81"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 14.68725 82.45287 24.82079 14.68725 29.29299</code></pre> +<div class="sourceCode" id="cb83"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">hs_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.298536 38.85371 11.69613 8.298536 15.71561</code></pre> +</div> +<div class="section level3"> +<h3 id="comparison-across-parent-models">Comparison across parent models<a class="anchor" aria-label="anchor" href="#comparison-across-parent-models"></a> +</h3> +<p>After model reduction for all models with pH influence, they are +compared with each other.</p> +<div class="sourceCode" id="cb85"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">sfo_pH</span>, <span class="va">fomc_pH_2</span>, <span class="va">dfop_pH_2</span>, <span class="va">dfop_pH_4</span>, <span class="va">sforb_pH_2</span>, <span class="va">hs_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>Data: 116 observations of 1 variable(s) grouped in 18 datasets + + npar AIC BIC Lik +sfo_pH 5 783.09 787.54 -386.54 +fomc_pH_2 6 767.49 772.83 -377.75 +dfop_pH_4 7 767.35 773.58 -376.68 +sforb_pH_2 7 770.94 777.17 -378.47 +dfop_pH_2 8 765.14 772.26 -374.57 +hs_pH_2 10 766.47 775.37 -373.23</code></pre> +<p>The DFOP model with pH influence on <code>k2</code> and +<code>g</code> and a random effect only on <code>k2</code> is finally +selected as the best fit.</p> +<p>The endpoints resulting from this model are listed below. Please +refer to the Appendix for a detailed listing.</p> +<div class="sourceCode" id="cb87"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +50% 5.75 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 18.36876 73.51841 22.13125 4.191901 23.98672</code></pre> +<div class="sourceCode" id="cb89"><pre class="downlit sourceCode r"> +<code class="sourceCode R"><span><span class="fu"><a href="../../reference/endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">dfop_pH_2</span>, covariates <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>pH <span class="op">=</span> <span class="fl">7</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<pre><code>$covariates + pH +User 7 + +$distimes + DT50 DT90 DT50back DT50_k1 DT50_k2 +meso 8.346428 28.34437 8.532507 4.191901 8.753618</code></pre> +</div> +</div> +<div class="section level2"> +<h2 id="conclusions">Conclusions<a class="anchor" aria-label="anchor" href="#conclusions"></a> +</h2> +<p>These evaluations demonstrate that covariate effects can be included +for all types of parent degradation models. These models can then be +further refined to make them fully identifiable.</p> +</div> +<div class="section level2"> +<h2 id="appendix">Appendix<a class="anchor" aria-label="anchor" href="#appendix"></a> +</h2> +<div class="section level3"> +<h3 id="hierarchical-fit-listings">Hierarchical fit listings<a class="anchor" aria-label="anchor" href="#hierarchical-fit-listings"></a> +</h3> +<div class="section level4"> +<h4 id="fits-without-covariate-effects">Fits without covariate effects<a class="anchor" aria-label="anchor" href="#fits-without-covariate-effects"></a> +</h4> + +</div> +<div class="section level4"> +<h4 id="fits-with-covariate-effects">Fits with covariate effects<a class="anchor" aria-label="anchor" href="#fits-with-covariate-effects"></a> +</h4> + +</div> +</div> +<div class="section level3"> +<h3 id="session-info">Session info<a class="anchor" aria-label="anchor" href="#session-info"></a> +</h3> +<pre><code>R version 4.3.1 (2023-06-16) +Platform: x86_64-pc-linux-gnu (64-bit) +Running under: Debian GNU/Linux 12 (bookworm) + +Matrix products: default +BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 +LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0 + +locale: + [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C + [3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8 + [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8 + [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C + [9] LC_ADDRESS=C LC_TELEPHONE=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C + +time zone: Europe/Berlin +tzcode source: system (glibc) + +attached base packages: +[1] parallel stats graphics grDevices utils datasets methods +[8] base + +other attached packages: +[1] saemix_3.2 npde_3.3 knitr_1.43 mkin_1.2.6 + +loaded via a namespace (and not attached): + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.20-45 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.1 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 +[13] jsonlite_1.8.5 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.1 memoise_2.0.1 +[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 +[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 +[37] fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 +[41] pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 gtable_0.3.3 +[45] glue_1.6.2 systemfonts_1.0.4 highr_0.10 xfun_0.39 +[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 +[53] nlme_3.1-162 rmarkdown_2.22 compiler_4.3.1 readxl_1.4.2 </code></pre> +</div> +<div class="section level3"> +<h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> +</h3> +<pre><code>CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz</code></pre> +<pre><code>MemTotal: 12165632 kB</code></pre> +</div> +</div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + + <nav id="toc" 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class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/FOCUS_Z.rmd" class="external-link"><code>vignettes/web_only/FOCUS_Z.rmd</code></a></small> <div class="hidden name"><code>FOCUS_Z.rmd</code></div> diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html index 9feecfce..e4e457fc 100644 --- a/docs/dev/articles/web_only/NAFTA_examples.html +++ b/docs/dev/articles/web_only/NAFTA_examples.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ to the US EPA SOP for the NAFTA guidance</h1> Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-04-16)</h4> +2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/NAFTA_examples.rmd" class="external-link"><code>vignettes/web_only/NAFTA_examples.rmd</code></a></small> <div class="hidden name"><code>NAFTA_examples.rmd</code></div> diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index 87bdd55f..b3c12f66 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -135,7 +135,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-04-16)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/benchmarks.rmd" class="external-link"><code>vignettes/web_only/benchmarks.rmd</code></a></small> <div class="hidden name"><code>benchmarks.rmd</code></div> @@ -423,8 +423,24 @@ models fitted to two datasets, i.e. eight fits for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.3</td> <td align="left">1.2.3</td> -<td align="right">1.404</td> -<td align="right">1.933</td> +<td align="right">1.406</td> +<td align="right">1.948</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">1.386</td> +<td align="right">1.960</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.5</td> +<td align="right">1.400</td> +<td align="right">1.936</td> </tr> </tbody> </table> @@ -649,9 +665,27 @@ for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.2.3</td> <td align="left">1.2.3</td> -<td align="right">0.797</td> -<td align="right">2.124</td> -<td align="right">1.182</td> +<td align="right">0.793</td> +<td align="right">2.109</td> +<td align="right">1.178</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.779</td> +<td align="right">2.080</td> +<td align="right">1.106</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.5</td> +<td align="right">0.800</td> +<td align="right">2.118</td> +<td align="right">1.172</td> </tr> </tbody> </table> @@ -958,11 +992,35 @@ dataset, i.e. one fit for each test.</p> <td align="left">4.2.3</td> <td align="left">1.2.3</td> <td align="right">0.432</td> -<td align="right">0.551</td> -<td align="right">0.616</td> -<td align="right">1.039</td> -<td align="right">0.734</td> -<td align="right">0.981</td> +<td align="right">0.549</td> +<td align="right">0.609</td> +<td align="right">1.052</td> +<td align="right">0.743</td> +<td align="right">0.989</td> +</tr> +<tr class="even"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.4</td> +<td align="right">0.410</td> +<td align="right">0.526</td> +<td align="right">0.553</td> +<td align="right">1.249</td> +<td align="right">0.712</td> +<td align="right">0.948</td> +</tr> +<tr class="odd"> +<td align="left">Linux</td> +<td align="left">Ryzen 9 7950X</td> +<td align="left">4.3.0</td> +<td align="left">1.2.5</td> +<td align="right">0.433</td> +<td align="right">0.558</td> +<td align="right">0.618</td> +<td align="right">1.053</td> +<td align="right">0.745</td> +<td align="right">0.986</td> </tr> </tbody> </table> diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index e7905860..a0b34dda 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -135,7 +135,7 @@ definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2023-04-16</h4> + <h4 data-toc-skip class="date">2023-05-19</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/compiled_models.rmd" class="external-link"><code>vignettes/web_only/compiled_models.rmd</code></a></small> <div class="hidden name"><code>compiled_models.rmd</code></div> @@ -214,10 +214,10 @@ solution is also implemented, which is included in the tests below.</p> <span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="st">"R package rbenchmark is not available"</span><span class="op">)</span></span> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 4 analytical 1 1.000 0.105</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.276 0.134</span></span> -<span><span class="co">## 2 Eigenvalue based 1 1.762 0.185</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 21.914 2.301</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.108</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.259 0.136</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.704 0.184</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 21.574 2.330</span></span></code></pre> <p>We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.</p> </div> @@ -248,12 +248,12 @@ compiled code is available.</p> <span><span class="op">}</span></span></code></pre></div> <pre><code><span><span class="co">## Temporary DLL for differentials generated and loaded</span></span></code></pre> <pre><code><span><span class="co">## test replications relative elapsed</span></span> -<span><span class="co">## 2 deSolve, compiled 1 1.000 0.176</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 23.938 4.213</span></span></code></pre> +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.178</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.708 4.220</span></span></code></pre> <p>Here we get a performance benefit of a factor of 24 using the version of the differential equation model compiled from C code!</p> -<p>This vignette was built with mkin 1.2.3 on</p> -<pre><code><span><span class="co">## R version 4.2.3 (2023-03-15)</span></span> +<p>This vignette was built with mkin 1.2.5 on</p> +<pre><code><span><span class="co">## R version 4.3.0 (2023-04-21)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> <span><span class="co">## Running under: Debian GNU/Linux 12 (bookworm)</span></span></code></pre> <pre><code><span><span class="co">## CPU model: AMD Ryzen 9 7950X 16-Core Processor</span></span></code></pre> diff --git a/docs/dev/articles/web_only/dimethenamid_2018.html b/docs/dev/articles/web_only/dimethenamid_2018.html index eb4a11a5..60e65367 100644 --- a/docs/dev/articles/web_only/dimethenamid_2018.html +++ b/docs/dev/articles/web_only/dimethenamid_2018.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -136,7 +136,7 @@ from 2018</h1> Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 16 Apr 2023</h4> +built on 19 May 2023</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/dimethenamid_2018.rmd" class="external-link"><code>vignettes/web_only/dimethenamid_2018.rmd</code></a></small> <div class="hidden name"><code>dimethenamid_2018.rmd</code></div> @@ -615,13 +615,13 @@ satisfactory precision.</p> </h2> <div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> -<pre><code>R version 4.2.3 (2023-03-15) +<pre><code>R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 -LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so +BLAS: /usr/lib/x86_64-linux-gnu/openblas-serial/libblas.so.3 +LAPACK: /usr/lib/x86_64-linux-gnu/openblas-serial/libopenblas-r0.3.21.so; LAPACK version 3.11.0 locale: [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C @@ -631,27 +631,30 @@ locale: [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C +time zone: Europe/Berlin +tzcode source: system (glibc) + attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: -[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.3 knitr_1.42 +[1] saemix_3.2 npde_3.3 nlme_3.1-162 mkin_1.2.5 knitr_1.42 loaded via a namespace (and not attached): - [1] highr_0.10 pillar_1.9.0 bslib_0.4.2 compiler_4.2.3 - [5] jquerylib_0.1.4 tools_4.2.3 mclust_6.0.0 digest_0.6.31 - [9] tibble_3.2.1 jsonlite_1.8.4 evaluate_0.20 memoise_2.0.1 -[13] lifecycle_1.0.3 gtable_0.3.3 lattice_0.21-8 pkgconfig_2.0.3 -[17] rlang_1.1.0 DBI_1.1.3 cli_3.6.1 yaml_2.3.7 -[21] parallel_4.2.3 pkgdown_2.0.7 xfun_0.38 fastmap_1.1.1 -[25] gridExtra_2.3 dplyr_1.1.1 stringr_1.5.0 generics_0.1.3 -[29] desc_1.4.2 fs_1.6.1 vctrs_0.6.1 sass_0.4.5 -[33] systemfonts_1.0.4 tidyselect_1.2.0 rprojroot_2.0.3 lmtest_0.9-40 -[37] grid_4.2.3 glue_1.6.2 R6_2.5.1 textshaping_0.3.6 -[41] fansi_1.0.4 rmarkdown_2.21 purrr_1.0.1 ggplot2_3.4.2 -[45] magrittr_2.0.3 codetools_0.2-19 scales_1.2.1 htmltools_0.5.5 -[49] colorspace_2.1-0 ragg_1.2.5 utf8_1.2.3 stringi_1.7.12 -[53] munsell_0.5.0 cachem_1.0.7 zoo_1.8-12 </code></pre> + [1] sass_0.4.6 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 + [5] lattice_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 + [9] grid_4.3.0 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.4 +[13] DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 +[17] fansi_1.0.4 scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 +[21] jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 munsell_0.5.0 +[25] cachem_1.0.8 yaml_2.3.7 tools_4.3.0 parallel_4.3.0 +[29] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 +[33] vctrs_0.6.2 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 +[37] stringr_1.5.0 fs_1.6.2 ragg_1.2.5 pkgconfig_2.0.3 +[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 +[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 +[49] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 +[53] htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.0 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 2de5059c..7855f177 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -135,7 +135,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-04-20)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/multistart.rmd" class="external-link"><code>vignettes/web_only/multistart.rmd</code></a></small> <div class="hidden name"><code>multistart.rmd</code></div> diff --git a/docs/dev/articles/web_only/saem_benchmarks.html b/docs/dev/articles/web_only/saem_benchmarks.html index 66740a11..22acf655 100644 --- a/docs/dev/articles/web_only/saem_benchmarks.html +++ b/docs/dev/articles/web_only/saem_benchmarks.html @@ -34,7 +34,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -135,7 +135,7 @@ Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-04-16)</h4> +(rebuilt 2023-05-19)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/web_only/saem_benchmarks.rmd" class="external-link"><code>vignettes/web_only/saem_benchmarks.rmd</code></a></small> <div class="hidden name"><code>saem_benchmarks.rmd</code></div> @@ -398,10 +398,30 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.3</td> <td align="left">3.2</td> -<td align="right">1.389</td> -<td align="right">2.300</td> -<td align="right">1.880</td> -<td align="right">2.355</td> +<td align="right">1.419</td> +<td align="right">2.374</td> +<td align="right">1.926</td> +<td align="right">2.398</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">0.972</td> +<td align="right">2.550</td> +<td align="right">1.987</td> +<td align="right">2.055</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.5</td> +<td align="left">3.2</td> +<td align="right">0.994</td> +<td align="right">2.546</td> +<td align="right">1.999</td> +<td align="right">2.070</td> </tr> </tbody> </table> @@ -473,10 +493,30 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.3</td> <td align="left">3.2</td> -<td align="right">2.300</td> -<td align="right">3.075</td> -<td align="right">3.206</td> -<td align="right">3.471</td> +<td align="right">2.348</td> +<td align="right">3.134</td> +<td align="right">3.253</td> +<td align="right">3.530</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">2.127</td> +<td align="right">3.587</td> +<td align="right">3.433</td> +<td align="right">3.595</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.5</td> +<td align="left">3.2</td> +<td align="right">2.152</td> +<td align="right">3.316</td> +<td align="right">3.309</td> +<td align="right">3.337</td> </tr> </tbody> </table> @@ -540,8 +580,24 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.3</td> <td align="left">3.2</td> -<td align="right">12.951</td> -<td align="right">294.082</td> +<td align="right">12.841</td> +<td align="right">292.688</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">12.160</td> +<td align="right">265.934</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.5</td> +<td align="left">3.2</td> +<td align="right">11.249</td> +<td align="right">290.918</td> </tr> </tbody> </table> @@ -599,7 +655,21 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.3</td> <td align="left">3.2</td> -<td align="right">477.297</td> +<td align="right">483.027</td> +</tr> +<tr class="odd"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.4</td> +<td align="left">3.2</td> +<td align="right">456.252</td> +</tr> +<tr class="even"> +<td align="left">Ryzen 9 7950X</td> +<td align="left">Linux</td> +<td align="left">1.2.5</td> +<td align="left">3.2</td> +<td align="right">479.637</td> </tr> </tbody> </table> diff --git a/docs/dev/authors.html b/docs/dev/authors.html index 1e2fc48f..04f0daae 100644 --- a/docs/dev/authors.html +++ b/docs/dev/authors.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <a href="articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -132,13 +135,13 @@ <p>Ranke J (2023). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. -R package version 1.2.4, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. +R package version 1.2.6, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2023}, - note = {R package version 1.2.4}, + note = {R package version 1.2.6}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> diff --git a/docs/dev/index.html b/docs/dev/index.html index 59b78ff0..dde09ea8 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</span> </span> </div> @@ -86,6 +86,9 @@ <a href="articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 93207241..4e652b96 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> @@ -105,14 +108,24 @@ </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124">mkin 1.2.4<a class="anchor" aria-label="anchor" href="#mkin-124"></a></h2> +<h2 class="page-header" data-toc-text="1.2.6" id="mkin-126">mkin 1.2.6<a class="anchor" aria-label="anchor" href="#mkin-126"></a></h2> </div> <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.5" id="mkin-125">mkin 1.2.5<a class="anchor" aria-label="anchor" href="#mkin-125"></a></h2> +<ul><li><p>‘vignettes/mesotrione_parent_2023.rnw’: Prebuilt vignette showing how covariate modelling can be done for all relevant parent degradation models.</p></li> +<li><p>‘inst/testdata/mesotrione_soil_efsa_2016}.xlsx’: Another example spreadsheets for use with ‘read_spreadsheet()’, featuring pH dependent degradation</p></li> +<li><p>R/illparms.R: Fix the detection of ill-defined slope or error model parameters for the case that the estimate is negative</p></li> +</ul></div> + <div class="section level2"> +<h2 class="page-header" data-toc-text="1.2.4" id="mkin-124">mkin 1.2.4<a class="anchor" aria-label="anchor" href="#mkin-124"></a></h2> +<ul><li>R/endpoints.R: Fix the calculation of endpoints for user specified covariate values</li> +</ul></div> + <div class="section level2"> <h2 class="page-header" data-toc-text="1.2.3.1" id="mkin-1231-unreleased">mkin 1.2.3.1 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-1231-unreleased"></a></h2> <ul><li>Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123">mkin 1.2.3<a class="anchor" aria-label="anchor" href="#mkin-123"></a></h2> +<h2 class="page-header" data-toc-text="1.2.3" id="mkin-123-2023-04-17">mkin 1.2.3 (2023-04-17)<a class="anchor" aria-label="anchor" href="#mkin-123-2023-04-17"></a></h2> <ul><li><p>‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits.</p></li> <li><p>Depend on current deSolve version with the possibility to avoid resolving symbols in a shared library (compiled models) over and over, thanks to Thomas Petzoldt.</p></li> <li><p>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Start a new cluster after creating a model stored in the user specified location, because otherwise symbols are not found by the worker processes.</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index c3829f60..e8d8b1eb 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -8,6 +8,7 @@ articles: 2022_cyan_pathway: prebuilt/2022_cyan_pathway.html 2022_dmta_parent: prebuilt/2022_dmta_parent.html 2022_dmta_pathway: prebuilt/2022_dmta_pathway.html + 2023_mesotrione_parent: prebuilt/2023_mesotrione_parent.html twa: twa.html FOCUS_Z: web_only/FOCUS_Z.html NAFTA_examples: web_only/NAFTA_examples.html @@ -16,7 +17,7 @@ articles: dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html saem_benchmarks: web_only/saem_benchmarks.html -last_built: 2023-04-20T18:24Z +last_built: 2023-08-10T05:34Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/AIC.mmkin.html b/docs/dev/reference/AIC.mmkin.html index ebfe052d..1179c7ac 100644 --- a/docs/dev/reference/AIC.mmkin.html +++ b/docs/dev/reference/AIC.mmkin.html @@ -18,7 +18,7 @@ same dataset."><meta name="robots" content="noindex"><!-- mathjax --><script src </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/CAKE_export.html b/docs/dev/reference/CAKE_export.html index 7b52a8c5..3b6f23fc 100644 --- a/docs/dev/reference/CAKE_export.html +++ b/docs/dev/reference/CAKE_export.html @@ -18,7 +18,7 @@ specified as well."><meta name="robots" content="noindex"><!-- mathjax --><scrip </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html index 8af0a8e2..52c51b25 100644 --- a/docs/dev/reference/D24_2014.html +++ b/docs/dev/reference/D24_2014.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -132,7 +132,7 @@ constrained by data protection regulations.</p> <p>Hellenic Ministry of Rural Development and Agriculture (2014) Final addendum to the Renewal Assessment Report - public version - 2,4-D Volume 3 Annex B.8 Fate and behaviour in the environment -<a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</a></p> +https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p> </div> <div id="details"> <h2>Details</h2> diff --git a/docs/dev/reference/DFOP.solution.html b/docs/dev/reference/DFOP.solution.html index d462133c..5b566de0 100644 --- a/docs/dev/reference/DFOP.solution.html +++ b/docs/dev/reference/DFOP.solution.html @@ -18,7 +18,7 @@ two exponential decline functions."><meta name="robots" content="noindex"><!-- m </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/Extract.mmkin.html b/docs/dev/reference/Extract.mmkin.html index 3a22d14b..1f8de281 100644 --- a/docs/dev/reference/Extract.mmkin.html +++ b/docs/dev/reference/Extract.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html index a8eb25cf..bef6155d 100644 --- a/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/dev/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -21,7 +21,7 @@ in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html index 24297c78..193418fa 100644 --- a/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html index caf258ba..a9549122 100644 --- a/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html index bc3d1c08..52bef6cf 100644 --- a/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/dev/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -21,7 +21,7 @@ in this fit."><meta name="robots" content="noindex"><!-- mathjax --><script src= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOCUS_2006_datasets.html b/docs/dev/reference/FOCUS_2006_datasets.html index 78f8e81b..ca3bc313 100644 --- a/docs/dev/reference/FOCUS_2006_datasets.html +++ b/docs/dev/reference/FOCUS_2006_datasets.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/FOMC.solution.html b/docs/dev/reference/FOMC.solution.html index e1813261..ed190bae 100644 --- a/docs/dev/reference/FOMC.solution.html +++ b/docs/dev/reference/FOMC.solution.html @@ -18,7 +18,7 @@ a decreasing rate constant."><meta name="robots" content="noindex"><!-- mathjax </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/HS.solution.html b/docs/dev/reference/HS.solution.html index d42eaef6..f0a15c45 100644 --- a/docs/dev/reference/HS.solution.html +++ b/docs/dev/reference/HS.solution.html @@ -18,7 +18,7 @@ between them."><meta name="robots" content="noindex"><!-- mathjax --><script src </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/IORE.solution.html b/docs/dev/reference/IORE.solution.html index b9d4734f..458e52d0 100644 --- a/docs/dev/reference/IORE.solution.html +++ b/docs/dev/reference/IORE.solution.html @@ -18,7 +18,7 @@ a concentration dependent rate constant."><meta name="robots" content="noindex"> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/NAFTA_SOP_2015.html b/docs/dev/reference/NAFTA_SOP_2015.html index 299863d7..329d476e 100644 --- a/docs/dev/reference/NAFTA_SOP_2015.html +++ b/docs/dev/reference/NAFTA_SOP_2015.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/NAFTA_SOP_Attachment.html b/docs/dev/reference/NAFTA_SOP_Attachment.html index 6bc86b46..c9874b5b 100644 --- a/docs/dev/reference/NAFTA_SOP_Attachment.html +++ b/docs/dev/reference/NAFTA_SOP_Attachment.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex 70d084a3..5de2bdc7 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 0f7d4405..556ca0a7 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/SFO.solution.html b/docs/dev/reference/SFO.solution.html index 08e031e7..42cd16a0 100644 --- a/docs/dev/reference/SFO.solution.html +++ b/docs/dev/reference/SFO.solution.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/SFORB.solution.html b/docs/dev/reference/SFORB.solution.html index 7e584ace..4be4983f 100644 --- a/docs/dev/reference/SFORB.solution.html +++ b/docs/dev/reference/SFORB.solution.html @@ -21,7 +21,7 @@ and no substance in the bound fraction."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/add_err.html b/docs/dev/reference/add_err.html index 57db40d1..66220dd6 100644 --- a/docs/dev/reference/add_err.html +++ b/docs/dev/reference/add_err.html @@ -19,7 +19,7 @@ may depend on the predicted value and is specified as a standard deviation."><me </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index 39a30dff..f9153a80 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -20,7 +20,7 @@ the model on the previous line."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index fc5ff777..14aa5ef1 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/confint.mkinfit.html b/docs/dev/reference/confint.mkinfit.html index a3571fa5..4945be22 100644 --- a/docs/dev/reference/confint.mkinfit.html +++ b/docs/dev/reference/confint.mkinfit.html @@ -24,7 +24,7 @@ method of Venzon and Moolgavkar (1988)."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -254,7 +254,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="va">f_d_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/system.time.html" class="external-link">system.time</a></span><span class="op">(</span><span class="va">ci_profile</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f_d_1</span>, method <span class="op">=</span> <span class="st">"profile"</span>, cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.183 0.000 1.182 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.239 0.000 1.239 </span> <span class="r-in"><span><span class="co"># Using more cores does not save much time here, as parent_0 takes up most of the time</span></span></span> <span class="r-in"><span><span class="co"># If we additionally exclude parent_0 (the confidence of which is often of</span></span></span> <span class="r-in"><span><span class="co"># minor interest), we get a nice performance improvement if we use at least 4 cores</span></span></span> @@ -262,7 +262,7 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"k_parent_sink"</span>, <span class="st">"k_parent_m1"</span>, <span class="st">"k_m1_sink"</span>, <span class="st">"sigma"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="va">n_cores</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Profiling the likelihood</span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 0.418 0.116 0.294 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.428 0.109 0.290 </span> <span class="r-in"><span><span class="va">ci_profile</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> <span class="r-out co"><span class="r-pr">#></span> parent_0 96.456003640 1.027703e+02</span> diff --git a/docs/dev/reference/create_deg_func.html b/docs/dev/reference/create_deg_func.html index fd8325c0..deeb2246 100644 --- a/docs/dev/reference/create_deg_func.html +++ b/docs/dev/reference/create_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -148,8 +148,8 @@ <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.235 1.000 0.235 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.294 1.251 0.294 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.244 1.000 0.245 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.304 1.246 0.303 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> @@ -162,8 +162,8 @@ <span class="r-in"><span> deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> <span class="r-in"><span> replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test replications elapsed relative user.self sys.self user.child</span> -<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.374 1.000 0.374 0 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.527 1.409 0.526 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.386 1.000 0.386 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.537 1.391 0.537 0 0</span> <span class="r-out co"><span class="r-pr">#></span> sys.child</span> <span class="r-out co"><span class="r-pr">#></span> 1 0</span> <span class="r-out co"><span class="r-pr">#></span> 2 0</span> diff --git a/docs/dev/reference/dimethenamid_2018.html b/docs/dev/reference/dimethenamid_2018.html index 0fcd0c61..5a39602c 100644 --- a/docs/dev/reference/dimethenamid_2018.html +++ b/docs/dev/reference/dimethenamid_2018.html @@ -22,7 +22,7 @@ constrained by data protection regulations."><meta name="robots" content="noinde </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -132,7 +132,7 @@ constrained by data protection regulations.</p> <p>Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate and behaviour Rev. 2 - November 2017 -<a href="https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716" class="external-link">https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</a></p> +https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</p> </div> <div id="details"> <h2>Details</h2> @@ -222,10 +222,10 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$so, plot.type = "convergence")</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_dmta_saem_tc</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:30:03 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:30:03 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:28:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:28:53 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_DMTA/dt = - k_DMTA * DMTA</span> @@ -238,7 +238,7 @@ specific pieces of information in the comments.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 304.528 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 299.056 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 9 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/dev/reference/ds_mixed.html b/docs/dev/reference/ds_mixed.html index 2d0274ff..f60df25b 100644 --- a/docs/dev/reference/ds_mixed.html +++ b/docs/dev/reference/ds_mixed.html @@ -18,7 +18,7 @@ the 'dataset_generation' directory."><meta name="robots" content="noindex"><!-- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/endpoints.html b/docs/dev/reference/endpoints.html index 3cda0f3c..3455275a 100644 --- a/docs/dev/reference/endpoints.html +++ b/docs/dev/reference/endpoints.html @@ -23,7 +23,7 @@ advantage that the SFORB model can also be used for metabolites."><meta name="ro </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/experimental_data_for_UBA.html b/docs/dev/reference/experimental_data_for_UBA.html index 77ff6ce4..c0d029cc 100644 --- a/docs/dev/reference/experimental_data_for_UBA.html +++ b/docs/dev/reference/experimental_data_for_UBA.html @@ -45,7 +45,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/f_time_norm_focus.html b/docs/dev/reference/f_time_norm_focus.html index b0722bc6..69578b89 100644 --- a/docs/dev/reference/f_time_norm_focus.html +++ b/docs/dev/reference/f_time_norm_focus.html @@ -18,7 +18,7 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369)."><meta name=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/focus_soil_moisture.html b/docs/dev/reference/focus_soil_moisture.html index cb4a035a..d72e48b1 100644 --- a/docs/dev/reference/focus_soil_moisture.html +++ b/docs/dev/reference/focus_soil_moisture.html @@ -18,7 +18,7 @@ corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5."><meta name="robots" con </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/get_deg_func.html b/docs/dev/reference/get_deg_func.html index cf81a591..7cc1cd24 100644 --- a/docs/dev/reference/get_deg_func.html +++ b/docs/dev/reference/get_deg_func.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/hierarchical_kinetics.html b/docs/dev/reference/hierarchical_kinetics.html index 7ece90cc..4da1e94f 100644 --- a/docs/dev/reference/hierarchical_kinetics.html +++ b/docs/dev/reference/hierarchical_kinetics.html @@ -24,7 +24,7 @@ includes them.'><meta name="robots" content="noindex"><!-- mathjax --><script sr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/illparms.html b/docs/dev/reference/illparms.html index 7bf6c1fe..2dffcfe9 100644 --- a/docs/dev/reference/illparms.html +++ b/docs/dev/reference/illparms.html @@ -21,7 +21,7 @@ without parameter transformations is used."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/ilr.html b/docs/dev/reference/ilr.html index 94b23a76..677c3f5e 100644 --- a/docs/dev/reference/ilr.html +++ b/docs/dev/reference/ilr.html @@ -18,7 +18,7 @@ transformations."><meta name="robots" content="noindex"><!-- mathjax --><script </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index d1b789c3..d6f859e5 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.6</span> </span> </div> @@ -54,6 +54,9 @@ <a href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> </li> <li> + <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + </li> + <li> <a href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> </li> <li> diff --git a/docs/dev/reference/intervals.saem.mmkin.html b/docs/dev/reference/intervals.saem.mmkin.html index a566ee8d..9eefd1c1 100644 --- a/docs/dev/reference/intervals.saem.mmkin.html +++ b/docs/dev/reference/intervals.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/llhist.html b/docs/dev/reference/llhist.html index 2b5afa25..4250ca39 100644 --- a/docs/dev/reference/llhist.html +++ b/docs/dev/reference/llhist.html @@ -18,7 +18,7 @@ original fit is shown as a red vertical line."><meta name="robots" content="noin </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/loftest.html b/docs/dev/reference/loftest.html index 871dfc88..c11fe007 100644 --- a/docs/dev/reference/loftest.html +++ b/docs/dev/reference/loftest.html @@ -20,7 +20,7 @@ lrtest.default from the lmtest package."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/logLik.mkinfit.html b/docs/dev/reference/logLik.mkinfit.html index e51a52eb..bbe44051 100644 --- a/docs/dev/reference/logLik.mkinfit.html +++ b/docs/dev/reference/logLik.mkinfit.html @@ -21,7 +21,7 @@ the error model."><meta name="robots" content="noindex"><!-- mathjax --><script </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/logLik.saem.mmkin.html b/docs/dev/reference/logLik.saem.mmkin.html index 6d0102c1..fc97386c 100644 --- a/docs/dev/reference/logLik.saem.mmkin.html +++ b/docs/dev/reference/logLik.saem.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/logistic.solution.html b/docs/dev/reference/logistic.solution.html index 9cfebf03..f161823c 100644 --- a/docs/dev/reference/logistic.solution.html +++ b/docs/dev/reference/logistic.solution.html @@ -18,7 +18,7 @@ an increasing rate constant, supposedly caused by microbial growth"><meta name=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/lrtest.mkinfit.html b/docs/dev/reference/lrtest.mkinfit.html index d59590c0..32b7cf76 100644 --- a/docs/dev/reference/lrtest.mkinfit.html +++ b/docs/dev/reference/lrtest.mkinfit.html @@ -21,7 +21,7 @@ and can be expressed by fixing the parameters of the other."><meta name="robots" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/max_twa_parent.html b/docs/dev/reference/max_twa_parent.html index 507a0758..40a29918 100644 --- a/docs/dev/reference/max_twa_parent.html +++ b/docs/dev/reference/max_twa_parent.html @@ -23,7 +23,7 @@ soil section of the FOCUS guidance."><meta name="robots" content="noindex"><!-- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mccall81_245T.html b/docs/dev/reference/mccall81_245T.html index c0e9cb37..70e96537 100644 --- a/docs/dev/reference/mccall81_245T.html +++ b/docs/dev/reference/mccall81_245T.html @@ -19,7 +19,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mean_degparms.html b/docs/dev/reference/mean_degparms.html index a374d532..0a52af76 100644 --- a/docs/dev/reference/mean_degparms.html +++ b/docs/dev/reference/mean_degparms.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mhmkin.html b/docs/dev/reference/mhmkin.html index b41c11df..3e0a8c31 100644 --- a/docs/dev/reference/mhmkin.html +++ b/docs/dev/reference/mhmkin.html @@ -22,7 +22,7 @@ mixed-effects model fitting functions."><meta name="robots" content="noindex"><! </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mixed.html b/docs/dev/reference/mixed.html index 1709944a..e354315b 100644 --- a/docs/dev/reference/mixed.html +++ b/docs/dev/reference/mixed.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkin_long_to_wide.html b/docs/dev/reference/mkin_long_to_wide.html index 990506b5..4e7b2756 100644 --- a/docs/dev/reference/mkin_long_to_wide.html +++ b/docs/dev/reference/mkin_long_to_wide.html @@ -19,7 +19,7 @@ variable and several dependent variables as columns."><meta name="robots" conten </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkin_wide_to_long.html b/docs/dev/reference/mkin_wide_to_long.html index a324d3b8..5e419cbe 100644 --- a/docs/dev/reference/mkin_wide_to_long.html +++ b/docs/dev/reference/mkin_wide_to_long.html @@ -19,7 +19,7 @@ mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src="htt </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinds.html b/docs/dev/reference/mkinds.html index 6219766e..3c1154a8 100644 --- a/docs/dev/reference/mkinds.html +++ b/docs/dev/reference/mkinds.html @@ -20,7 +20,7 @@ provided by this package come as mkinds objects nevertheless."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkindsg.html b/docs/dev/reference/mkindsg.html index 6e221a23..4ef380cb 100644 --- a/docs/dev/reference/mkindsg.html +++ b/docs/dev/reference/mkindsg.html @@ -20,7 +20,7 @@ dataset if no data are supplied."><meta name="robots" content="noindex"><!-- mat </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinerrmin.html b/docs/dev/reference/mkinerrmin.html index 3a8b9610..205654d1 100644 --- a/docs/dev/reference/mkinerrmin.html +++ b/docs/dev/reference/mkinerrmin.html @@ -18,7 +18,7 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinerrplot.html b/docs/dev/reference/mkinerrplot.html index bc9b828a..e2d37adb 100644 --- a/docs/dev/reference/mkinerrplot.html +++ b/docs/dev/reference/mkinerrplot.html @@ -21,7 +21,7 @@ using the argument show_errplot = TRUE."><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html index 237d903e..aa714f26 100644 --- a/docs/dev/reference/mkinfit.html +++ b/docs/dev/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function."><meta name="robots" content="noindex"><!-- mathjax --><scr </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -401,10 +401,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># Use shorthand notation for parent only degradation</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu">mkinfit</span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:30:40 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:30:40 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:29:30 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:29:30 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -552,9 +552,9 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.236</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.263 0.298</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.373 0.560</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.241</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 1.270 0.306</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.382 0.574</span> <span class="r-in"><span><span class="co"># }</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span></span></span> @@ -581,10 +581,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>diag(.) had 0 or NA entries; non-finite result is doubtful</span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:30:44 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:30:44 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:29:35 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:29:35 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent</span> @@ -593,7 +593,7 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 0.688 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 3729 model solutions performed in 0.727 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html index 50ec64fa..3e74b37f 100644 --- a/docs/dev/reference/mkinmod.html +++ b/docs/dev/reference/mkinmod.html @@ -21,7 +21,7 @@ components."><meta name="robots" content="noindex"><!-- mathjax --><script src=" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -330,7 +330,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span>, full_name <span class="op">=</span> <span class="st">"Metabolite M1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> name <span class="op">=</span> <span class="st">"SFO_SFO"</span>, dll_dir <span class="op">=</span> <span class="va">DLL_dir</span>, unload <span class="op">=</span> <span class="cn">TRUE</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> -<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/RtmpiGRJ6t/file5c7f7365e02a0.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmpo7fLwX/file774c3752c3c97.so to /home/jranke/.local/share/mkin/SFO_SFO.so</span> <span class="r-in"><span><span class="co"># Now we can save the model and restore it in a new session</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/readRDS.html" class="external-link">saveRDS</a></span><span class="op">(</span><span class="va">SFO_SFO.2</span>, file <span class="op">=</span> <span class="st">"~/SFO_SFO.rds"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Terminate the R session here if you would like to check, and then do</span></span></span> @@ -383,7 +383,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-out co"><span class="r-pr">#></span> })</span> <span class="r-out co"><span class="r-pr">#></span> return(predicted)</span> <span class="r-out co"><span class="r-pr">#></span> }</span> -<span class="r-out co"><span class="r-pr">#></span> <environment: 0x555558bd6708></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x55556118b9d0></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># If we have several parallel metabolites</span></span></span> <span class="r-in"><span><span class="co"># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span></span></span> diff --git a/docs/dev/reference/mkinparplot.html b/docs/dev/reference/mkinparplot.html index f7d404ef..297c3685 100644 --- a/docs/dev/reference/mkinparplot.html +++ b/docs/dev/reference/mkinparplot.html @@ -18,7 +18,7 @@ mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src="htt </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinplot.html b/docs/dev/reference/mkinplot.html index d83ea3f4..008fdd42 100644 --- a/docs/dev/reference/mkinplot.html +++ b/docs/dev/reference/mkinplot.html @@ -18,7 +18,7 @@ plot.mkinfit."><meta name="robots" content="noindex"><!-- mathjax --><script src </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mkinpredict.html b/docs/dev/reference/mkinpredict.html index 7d8e7c26..262b3fde 100644 --- a/docs/dev/reference/mkinpredict.html +++ b/docs/dev/reference/mkinpredict.html @@ -19,7 +19,7 @@ kinetic parameters and initial values for the state variables."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -394,12 +394,11 @@ as these always return mapped output.</p></dd> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">20</span>, by <span class="op">=</span> <span class="fl">0.1</span><span class="op">)</span>,</span></span> <span class="r-in"><span> solution_type <span class="op">=</span> <span class="st">"analytical"</span>, use_compiled <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span><span class="op">[</span><span class="fl">201</span>,<span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="op">}</span></span></span> -<span class="r-msg co"><span class="r-pr">#></span> Loading required package: rbenchmark</span> <span class="r-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.00 0.004</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 4.00 0.016</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 4.25 0.017</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 40.75 0.163</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.5 0.003</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.5 0.007</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 31.5 0.063</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Predict from a fitted model</span></span></span> diff --git a/docs/dev/reference/mkinresplot.html b/docs/dev/reference/mkinresplot.html index e73ac93c..2108778e 100644 --- a/docs/dev/reference/mkinresplot.html +++ b/docs/dev/reference/mkinresplot.html @@ -20,7 +20,7 @@ argument show_residuals = TRUE."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/mmkin.html b/docs/dev/reference/mmkin.html index 64623f20..4581129d 100644 --- a/docs/dev/reference/mmkin.html +++ b/docs/dev/reference/mmkin.html @@ -20,7 +20,7 @@ datasets specified in its first two arguments."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -206,10 +206,10 @@ plotting.</p></div> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">time_default</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 1.560 0.668 0.742 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.668 0.586 0.716 </span> <span class="r-in"><span><span class="va">time_1</span></span></span> <span class="r-out co"><span class="r-pr">#></span> user system elapsed </span> -<span class="r-out co"><span class="r-pr">#></span> 2.033 0.004 2.037 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.054 0.012 2.065 </span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu"><a href="endpoints.html">endpoints</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="st">"SFO_lin"</span>, <span class="fl">2</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> $ff</span> diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 6fc88621..ea847d32 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."><meta name="robots" content="noi </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.4</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/nafta.html b/docs/dev/reference/nafta.html index 6d568718..91cc716c 100644 --- a/docs/dev/reference/nafta.html +++ b/docs/dev/reference/nafta.html @@ -21,7 +21,7 @@ order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><m </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index 81c45ab9..49bad1a8 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -20,7 +20,7 @@ datasets. They are used internally by the nlme.mmkin() method."><meta name="robo </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index 76d667b9..bf520640 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -19,7 +19,7 @@ have been obtained by fitting the same model to a list of datasets."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/nobs.mkinfit.html b/docs/dev/reference/nobs.mkinfit.html index 10f6550b..fb6ce502 100644 --- a/docs/dev/reference/nobs.mkinfit.html +++ b/docs/dev/reference/nobs.mkinfit.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index d4175d41..b45423be 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."><meta nam </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index ee2ec7b2..d701438c 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 3d902b77..c5a67513 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -304,7 +304,7 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"><span><span class="va">f_nlmix</span> <span class="op"><-</span> <span class="fu">nlmix</span><span class="op">(</span><span class="va">f_obs</span><span class="op">)</span></span></span> <span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in nlmix(f_obs):</span> could not find function "nlmix"</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_nlmix</span><span class="op">)</span></span></span> -<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in plot(f_nlmix):</span> object 'f_nlmix' not found</span> +<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in eval(expr, envir, enclos):</span> object 'f_nlmix' not found</span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># We can overlay the two variants if we generate predictions</span></span></span> <span class="r-in"><span><span class="va">pred_nlme</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span></span> diff --git a/docs/dev/reference/plot.mkinfit.html b/docs/dev/reference/plot.mkinfit.html index 9cf12d82..42322156 100644 --- a/docs/dev/reference/plot.mkinfit.html +++ b/docs/dev/reference/plot.mkinfit.html @@ -19,7 +19,7 @@ observed data together with the solution of the fitted model."><meta name="robot </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/plot.mmkin.html b/docs/dev/reference/plot.mmkin.html index c8fde67c..e224ccf8 100644 --- a/docs/dev/reference/plot.mmkin.html +++ b/docs/dev/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><meta name="robots" </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/plot.nafta.html b/docs/dev/reference/plot.nafta.html index 8acaa8b3..1177dd81 100644 --- a/docs/dev/reference/plot.nafta.html +++ b/docs/dev/reference/plot.nafta.html @@ -18,7 +18,7 @@ function (SFO, then IORE, then DFOP)."><meta name="robots" content="noindex"><!- </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/read_spreadsheet.html b/docs/dev/reference/read_spreadsheet.html index 6e7203f4..cb2a0d0f 100644 --- a/docs/dev/reference/read_spreadsheet.html +++ b/docs/dev/reference/read_spreadsheet.html @@ -22,7 +22,7 @@ factors can be given in columns named 'Temperature' and 'Moisture'."><meta name= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/reexports.html b/docs/dev/reference/reexports.html index ee1148da..81563f52 100644 --- a/docs/dev/reference/reexports.html +++ b/docs/dev/reference/reexports.html @@ -28,7 +28,7 @@ intervals, nlme </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/residuals.mkinfit.html b/docs/dev/reference/residuals.mkinfit.html index 578b5066..f8b110b4 100644 --- a/docs/dev/reference/residuals.mkinfit.html +++ b/docs/dev/reference/residuals.mkinfit.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 9b9a911d..952e4eab 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."><meta name="robots" content="noindex </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -439,10 +439,10 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-plt img"><img src="saem-4.png" alt="" width="700" height="433"></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:32:32 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:32:32 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:31:33 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:31:33 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -457,7 +457,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 4.145 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.681 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Constant variance </span> diff --git a/docs/dev/reference/schaefer07_complex_case.html b/docs/dev/reference/schaefer07_complex_case.html index 880e5ac0..9e1eb3cf 100644 --- a/docs/dev/reference/schaefer07_complex_case.html +++ b/docs/dev/reference/schaefer07_complex_case.html @@ -19,7 +19,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 6f4ae169..0d4848b7 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."><meta name="robots" content= </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/sigma_twocomp.html b/docs/dev/reference/sigma_twocomp.html index 0ead0184..62160487 100644 --- a/docs/dev/reference/sigma_twocomp.html +++ b/docs/dev/reference/sigma_twocomp.html @@ -18,7 +18,7 @@ dependence of the measured value \(y\):"><meta name="robots" content="noindex">< </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index df3e3a44..3d0d7493 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index f627c2f6..b2bb592e 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values."><meta name="robots" content="noindex"><!-- mathjax --><script src="http </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -231,10 +231,10 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <h2>Examples</h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:34:39 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:34:39 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:33:37 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:33:37 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> diff --git a/docs/dev/reference/summary.mmkin.html b/docs/dev/reference/summary.mmkin.html index c27f1634..84cb51fd 100644 --- a/docs/dev/reference/summary.mmkin.html +++ b/docs/dev/reference/summary.mmkin.html @@ -18,7 +18,7 @@ and gives an overview of ill-defined parameters calculated by illparms."><meta n </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -152,7 +152,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span> quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fits</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.509 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.515 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Status:</span> <span class="r-out co"><span class="r-pr">#></span> dataset</span> diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index cb2c20bd..9e6ca376 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -252,10 +252,10 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span><span class="va">f_nlme</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> nlme version used for fitting: 3.1.162 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:34:41 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:34:41 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:33:40 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:33:40 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -265,7 +265,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.194 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.19 s using 4 iterations</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html index e434ad8d..fbd9e027 100644 --- a/docs/dev/reference/summary.saem.mmkin.html +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -330,10 +330,10 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> b.1 0.06363957 0.07878001 0.09392044</span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_saem_dfop_sfo_2</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> saemix version used for fitting: 3.2 </span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:34:58 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:34:58 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:33:55 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:33:55 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *</span> @@ -348,7 +348,7 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.384 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.133 s</span> <span class="r-out co"><span class="r-pr">#></span> Using 300, 100 iterations and 10 chains</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Variance model: Two-component variance function </span> diff --git a/docs/dev/reference/summary_listing.html b/docs/dev/reference/summary_listing.html index e584416a..640d834a 100644 --- a/docs/dev/reference/summary_listing.html +++ b/docs/dev/reference/summary_listing.html @@ -18,7 +18,7 @@ option results = "asis".'><meta name="robots" content="noindex"><!-- mathjax --> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/synthetic_data_for_UBA_2014.html b/docs/dev/reference/synthetic_data_for_UBA_2014.html index b8154c47..0ec5e832 100644 --- a/docs/dev/reference/synthetic_data_for_UBA_2014.html +++ b/docs/dev/reference/synthetic_data_for_UBA_2014.html @@ -32,7 +32,7 @@ Compare also the code in the example section to see the degradation models."><me </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> @@ -269,10 +269,10 @@ Compare also the code in the example section to see the degradation models."><me <span class="r-in"><span> <span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="synthetic_data_for_UBA_2014-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> -<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.2.3 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Sun Apr 16 08:35:08 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Sun Apr 16 08:35:08 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for fitting: 1.2.5 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.0 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Fri May 19 17:34:06 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Fri May 19 17:34:06 2023 </span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Equations:</span> <span class="r-out co"><span class="r-pr">#></span> d_parent/dt = - k_parent * parent</span> @@ -281,7 +281,7 @@ Compare also the code in the example section to see the degradation models."><me <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type deSolve </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.166 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 833 model solutions performed in 0.164 s</span> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Error model: Constant variance </span> <span class="r-out co"><span class="r-pr">#></span> </span> diff --git a/docs/dev/reference/test_data_from_UBA_2014.html b/docs/dev/reference/test_data_from_UBA_2014.html index 8b0194f6..fd5caf4e 100644 --- a/docs/dev/reference/test_data_from_UBA_2014.html +++ b/docs/dev/reference/test_data_from_UBA_2014.html @@ -18,7 +18,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/transform_odeparms.html b/docs/dev/reference/transform_odeparms.html index 4cb2e575..9e81258a 100644 --- a/docs/dev/reference/transform_odeparms.html +++ b/docs/dev/reference/transform_odeparms.html @@ -22,7 +22,7 @@ the ilr transformation is used."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/reference/update.mkinfit.html b/docs/dev/reference/update.mkinfit.html index 90aa0edb..fc644f6f 100644 --- a/docs/dev/reference/update.mkinfit.html +++ b/docs/dev/reference/update.mkinfit.html @@ -20,7 +20,7 @@ override these starting values."><meta name="robots" content="noindex"><!-- math </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.2.5</span> </span> </div> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index b3542d0b..c9ed0542 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -28,6 +28,9 @@ <loc>https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/articles/twa.html</loc> </url> <url> diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex c8f72a17..419192da 100644 --- a/vignettes/web_only/mkin_benchmarks.rda +++ b/vignettes/web_only/mkin_benchmarks.rda diff --git a/vignettes/web_only/saem_benchmarks.rda b/vignettes/web_only/saem_benchmarks.rda Binary files differindex 9e5ce2c3..52d623f2 100644 --- a/vignettes/web_only/saem_benchmarks.rda +++ b/vignettes/web_only/saem_benchmarks.rda |
